diff --git a/README.md b/README.md index 7b4ee04d8..30e9decc6 100644 --- a/README.md +++ b/README.md @@ -614,6 +614,10 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key | *fp_style == cp2k* | **user_fp_params** | Dict | |Parameters for cp2k calculation. find detail in manual.cp2k.org. only the kind section must be set before use. we assume that you have basic knowledge for cp2k input. | **external_input_path** | String | | Conflict with key:user_fp_params, use the template input provided by user, some rules should be followed, read the following text in detail. +| *fp_style == ABACUS* +| **user_fp_params** | Dict | |Parameters for ABACUS INPUT. find detail [Here](https://github.com/deepmodeling/abacus-develop/blob/develop/docs/input-main.md#out-descriptor). If `deepks_model` is set, the model file should be in the pseudopotential directory. +| **fp_orb_files** | List | |List of atomic orbital files. The files should be in pseudopotential directory. +| **fp_dpks_descriptor** | String | |DeePKS descriptor file name. The file should be in pseudopotential directory. One can choose the model-deviation engine by specifying the key `model_devi_engine`. If `model_devi_engine` is not specified, the default model-deviation engine will be LAMMPS. diff --git a/dpgen/data/gen.py b/dpgen/data/gen.py index 1e3cba355..43932bd80 100644 --- a/dpgen/data/gen.py +++ b/dpgen/data/gen.py @@ -136,15 +136,28 @@ def stru_ele(supercell_stru, stru_out, eles, natoms, jdata, path_work): for iatom in range(natoms[iele]): supercell_stru["types"].append(iele) pp_file_names = [os.path.basename(a) for a in jdata['potcars']] + orb_file_names = None + dpks_descriptor_name = None + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor']) supercell_stru["atom_masses"] = jdata["atom_masses"] supercell_stru["atom_names"] = eles - stru_text = make_abacus_scf_stru(supercell_stru, pp_file_names) + stru_text = make_abacus_scf_stru(supercell_stru, pp_file_names, orb_file_names, dpks_descriptor_name) with open(stru_out, "w") as f: f.write(stru_text) absolute_pp_file_path = [os.path.abspath(a) for a in jdata["potcars"]] + if 'orb_files' in jdata: + absolute_orb_file_path = [os.path.abspath(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + absolute_dpks_descriptor_path = os.path.abspath(jdata['dpks_descriptor']) for ipp, pp_file in enumerate(absolute_pp_file_path): os.symlink(pp_file, os.path.join(path_work, pp_file_names[ipp])) - + if 'orb_files' in jdata: + os.symlink(absolute_orb_file_path[ipp], os.path.join(path_work, orb_file_names[ipp])) + if 'dpks_descriptor' in jdata: + os.symlink(absolute_dpks_descriptor_path, os.path.join(path_work, dpks_descriptor_name)) def poscar_natoms(lines) : numb_atoms = 0 @@ -217,7 +230,14 @@ def poscar_scale_abacus(poscar_in, poscar_out, scale, jdata): stru["cells"] *= scale stru["coords"] *= scale pp_files = [os.path.basename(a) for a in jdata['potcars']] - ret = make_abacus_scf_stru(stru, pp_files) + orb_file_names = None + dpks_descriptor_name = None + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor']) + ret = make_abacus_scf_stru(stru, pp_files, orb_file_names, dpks_descriptor_name) + #ret = make_abacus_scf_stru(stru, pp_files) with open(poscar_out, "w") as fp: fp.write(ret) @@ -351,7 +371,13 @@ def make_super_cell_STRU(jdata) : from_struct=get_abacus_STRU(from_file, n_ele=len(jdata["elements"])) from_struct = make_supercell_abacus(from_struct, super_cell) pp_file_names = [os.path.basename(a) for a in jdata['potcars']] - stru_text = make_abacus_scf_stru(from_struct, pp_file_names) + orb_file_names = None + dpks_descriptor_name = None + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor']) + stru_text = make_abacus_scf_stru(from_struct, pp_file_names, orb_file_names, dpks_descriptor_name) with open(to_file, "w") as fp: fp.write(stru_text) # if kspacing is specified in json file, use kspacing to generate KPT (rather than directly using specified KPT). @@ -372,12 +398,20 @@ def make_super_cell_STRU(jdata) : create_path(path_work) cwd = os.getcwd() absolute_pp_file_path = [os.path.abspath(a) for a in jdata['potcars']] + if 'orb_files' in jdata: + absolute_orb_file_path = [os.path.abspath(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + absolute_dpks_descriptor_path = os.path.abspath(jdata['dpks_descriptor']) to_file = os.path.abspath(to_file) os.chdir(path_work) try: os.symlink(os.path.relpath(to_file), 'STRU') for ipp, pp_file in enumerate(absolute_pp_file_path): os.symlink(pp_file, pp_file_names[ipp]) # create pseudo-potential files + if 'orb_files' in jdata: + os.symlink(absolute_orb_file_path[ipp], orb_file_names[ipp]) + if 'dpks_descriptor' in jdata: + os.symlink(absolute_dpks_descriptor_path, dpks_descriptor_name) except FileExistsError: pass os.chdir(cwd) @@ -528,6 +562,13 @@ def make_abacus_relax (jdata, mdata) : jdata['relax_kpt'] = os.path.relpath(jdata['relax_kpt']) shutil.copy2( jdata['relax_kpt'], os.path.join(work_dir, 'KPT')) + + if "dpks_model" in jdata: + dpks_model_absolute_path = os.path.abspath(jdata["dpks_model"]) + assert(os.path.isfile(dpks_model_absolute_path)) + dpks_model_name = os.path.basename(jdata["dpks_model"]) + shutil.copy2( dpks_model_absolute_path, + os.path.join(work_dir, dpks_model_name)) os.chdir(work_dir) @@ -536,9 +577,13 @@ def make_abacus_relax (jdata, mdata) : os.chdir(ss) ln_src = os.path.relpath(os.path.join(work_dir,'INPUT')) kpt_src = os.path.relpath(os.path.join(work_dir,'KPT')) + if "dpks_model" in jdata: + ksmd_src = os.path.relpath(os.path.join(work_dir,dpks_model_name)) try: os.symlink(ln_src, 'INPUT') os.symlink(kpt_src, 'KPT') + if "dpks_model" in jdata: + os.symlink(ksmd_src, dpks_model_name) except FileExistsError: pass os.chdir(work_dir) @@ -624,6 +669,12 @@ def pert_scaled(jdata) : pert_atom = jdata['pert_atom'] pert_numb = jdata['pert_numb'] pp_file = [os.path.basename(a) for a in jdata['potcars']] + orb_file_names = None + dpks_descriptor_name = None + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor']) from_poscar = False if 'from_poscar' in jdata : from_poscar = jdata['from_poscar'] @@ -671,7 +722,7 @@ def pert_scaled(jdata) : stru_in = get_abacus_STRU(pos_in) stru_out = shuffle_stru_data(stru_in) with open(pos_out, "w") as fp: - fp.write(make_abacus_scf_stru(stru_out, pp_file)) + fp.write(make_abacus_scf_stru(stru_out, pp_file, orb_file_names, dpks_descriptor_name)) else : shutil.copy2(pos_in, pos_out) os.remove(pos_in) @@ -693,7 +744,7 @@ def pert_scaled(jdata) : stru_in = get_abacus_STRU(pos_in) stru_out = shuffle_stru_data(stru_in) with open(pos_out, "w") as fp: - fp.write(make_abacus_scf_stru(stru_out, pp_file)) + fp.write(make_abacus_scf_stru(stru_out, pp_file, orb_file_names, dpks_descriptor_name)) else : shutil.copy2(pos_in, pos_out) os.chdir(cwd) @@ -790,6 +841,28 @@ def make_abacus_md(jdata, mdata) : if 'md_kpt' in jdata: shutil.copy2(jdata['md_kpt'], os.path.join(path_md, 'KPT')) + orb_file_names = None + orb_file_abspath = None + dpks_descriptor_name = None + dpks_descriptor_abspath = None + dpks_model_name = None + dpks_model_abspath = None + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + orb_file_abspath = [os.path.abspath(a) for a in jdata['orb_files']] + for iorb, orb_file in enumerate(orb_file_names): + shutil.copy2(orb_file_abspath[iorb], + os.path.join(path_md, orb_file)) + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor']) + dpks_descriptor_abspath = os.path.abspath(jdata['dpks_descriptor']) + shutil.copy2(dpks_descriptor_abspath, + os.path.join(path_md, dpks_descriptor_name)) + if 'dpks_model' in jdata: + dpks_model_name = os.path.basename(jdata['dpks_model']) + dpks_model_abspath = os.path.abspath(jdata['dpks_model']) + shutil.copy2(dpks_model_abspath, + os.path.join(path_md, dpks_model_name)) for pp_file in jdata['potcars']: shutil.copy2(pp_file, os.path.join(path_md, os.path.basename(pp_file))) @@ -829,6 +902,13 @@ def make_abacus_md(jdata, mdata) : try: for pp_file in [os.path.basename(a) for a in jdata['potcars']]: os.symlink(os.path.relpath(os.path.join(path_md, pp_file)), pp_file) + if 'orb_files' in jdata: + for orb_file in orb_file_names: + os.symlink(os.path.relpath(os.path.join(path_md, orb_file)), orb_file) + if 'dpks_model' in jdata: + os.symlink(os.path.relpath(os.path.join(path_md, dpks_model_name)), dpks_model_name) + if 'dpks_descriptor' in jdata: + os.symlink(os.path.relpath(os.path.join(path_md, dpks_descriptor_name)), dpks_descriptor_name) except FileExistsError: pass @@ -1049,7 +1129,16 @@ def run_abacus_relax(jdata, mdata): #machine_type = mdata['fp_machine']['machine_type'] work_dir = os.path.join(jdata['out_dir'], global_dirname_02) pp_files = [os.path.basename(a) for a in jdata["potcars"]] - forward_files = ["STRU", "INPUT", "KPT"] + pp_files + orb_file_names = [] + dpks_descriptor_name = [] + dpks_model_name = [] + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])] + if 'dpks_model' in jdata: + dpks_model_name = [os.path.basename(jdata['dpks_model'])] + forward_files = ["STRU", "INPUT", "KPT"] + pp_files + orb_file_names + dpks_descriptor_name + dpks_model_name user_forward_files = mdata.get("fp" + "_user_forward_files", []) forward_files += [os.path.basename(file) for file in user_forward_files] backward_files = ["OUT.ABACUS"] @@ -1174,7 +1263,16 @@ def run_abacus_md(jdata, mdata): pert_numb = jdata['pert_numb'] md_nstep = jdata['md_nstep'] - forward_files = ["STRU", "INPUT", "KPT"] + orb_file_names = [] + dpks_descriptor_name = [] + dpks_model_name = [] + if 'orb_files' in jdata: + orb_file_names = [os.path.basename(a) for a in jdata['orb_files']] + if 'dpks_descriptor' in jdata: + dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])] + if 'dpks_model' in jdata: + dpks_model_name = [os.path.basename(jdata['dpks_model'])] + forward_files = ["STRU", "INPUT", "KPT"] + orb_file_names + dpks_descriptor_name + dpks_model_name for pp_file in [os.path.basename(a) for a in jdata['potcars']]: forward_files.append(pp_file) user_forward_files = mdata.get("fp" + "_user_forward_files", []) diff --git a/dpgen/data/tools/create_random_disturb.py b/dpgen/data/tools/create_random_disturb.py index 542a16096..67d507c64 100755 --- a/dpgen/data/tools/create_random_disturb.py +++ b/dpgen/data/tools/create_random_disturb.py @@ -220,7 +220,7 @@ def create_disturbs_abacus_dev(fin, nfile, dmax=1.0, etmax=0.1, ofmt="abacus", d # Writing it fout = fin + str(fid) + '.' + ofmt print("Creating %s ..." % fout) - ret = make_abacus_scf_stru(stru_d, stru_d['pp_files']) + ret = make_abacus_scf_stru(stru_d, stru_d['pp_files'], stru_d['orb_files'], stru_d['dpks_descriptor']) with open(fout, "w") as fp: fp.write(ret) if write_d: diff --git a/dpgen/generator/lib/abacus_scf.py b/dpgen/generator/lib/abacus_scf.py index fde813487..256eb1d9d 100644 --- a/dpgen/generator/lib/abacus_scf.py +++ b/dpgen/generator/lib/abacus_scf.py @@ -20,70 +20,74 @@ def make_abacus_scf_input(fp_params): # Make INPUT file for abacus pw scf calculation. ret = "INPUT_PARAMETERS\n" ret += "calculation scf\n" - assert(fp_params['ntype'] >= 0 and type(fp_params["ntype"]) == int), "'ntype' should be a positive integer." - ret += "ntype %d\n" % fp_params['ntype'] - #ret += "pseudo_dir ./\n" - if "ecutwfc" in fp_params: - assert(fp_params["ecutwfc"] >= 0) , "'ntype' should be non-negative." - ret += "ecutwfc %f\n" % fp_params["ecutwfc"] - if "dr2" in fp_params: - ret += "dr2 %e\n" % fp_params["dr2"] - if "niter" in fp_params: - assert(fp_params['niter'] >= 0 and type(fp_params["niter"])== int), "'niter' should be a positive integer." - ret += "niter %d\n" % fp_params["niter"] - if "basis_type" in fp_params: - assert(fp_params["basis_type"] in ["pw", "lcao", "lcao_in_pw"]) , "'basis_type' must in 'pw', 'lcao' or 'lcao_in_pw'." - ret+= "basis_type %s\n" % fp_params["basis_type"] - if "dft_functional" in fp_params: - ret += "dft_functional %s\n" % fp_params["dft_functional"] - if "gamma_only" in fp_params: - assert(fp_params["gamma_only"] ==1 ) , "'gamma_only' should be 1. Multi-k algorithm will be supported after the KPT generator is completed." - ret+= "gamma_only %d\n" % fp_params["gamma_only"] - if "mixing_type" in fp_params: - assert(fp_params["mixing_type"] in ["plain", "kerker", "pulay", "pulay-kerker", "broyden"]) - ret += "mixing_type %s\n" % fp_params["mixing_type"] - if "mixing_beta" in fp_params: - assert(fp_params["mixing_beta"] >= 0 and fp_params["mixing_beta"] < 1), "'mixing_beta' should between 0 and 1." - ret += "mixing_beta %f\n" % fp_params["mixing_beta"] - if "symmetry" in fp_params: - assert(fp_params["symmetry"] == 0 or fp_params["symmetry"] == 1), "'symmetry' should be either 0 or 1." - ret += "symmetry %d\n" % fp_params["symmetry"] - if "nbands" in fp_params: - assert(fp_params["nbands"] > 0 and type(fp_params["nbands"]) == int), "'nbands' should be a positive integer." - ret += "nbands %d\n" % fp_params["nbands"] - if "nspin" in fp_params: - assert(fp_params["nspin"] == 1 or fp_params["nspin"] == 2 or fp_params["nspin"] == 4), "'nspin' can anly take 1, 2 or 4" - ret += "nspin %d\n" % fp_params["nspin"] - if "ks_solver" in fp_params: - assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"]), "'ks_sover' should in 'cgx', 'dav', 'lapack', 'genelpa', 'hpseps', 'scalapack_gvx'." - ret += "ks_solver %s\n" % fp_params["ks_solver"] - if "smearing" in fp_params: - assert(fp_params["smearing"] in ["gaussian", "fd", "fixed", "mp", "mp2", "mv"]), "'smearing' should in 'gaussian', 'fd', 'fixed', 'mp', 'mp2', 'mv'. " - ret += "smearing %s\n" % fp_params["smearing"] - if "sigma" in fp_params: - assert(fp_params["sigma"] >= 0), "'sigma' should be non-negative." - ret += "sigma %f\n" % fp_params["sigma"] - if "force" in fp_params: - assert(fp_params["force"] == 0 or fp_params["force"] == 1), "'force' should be either 0 or 1." - ret += "force %d\n" % fp_params["force"] - if "stress" in fp_params: - assert(fp_params["stress"] == 0 or fp_params["stress"] == 1), "'stress' should be either 0 or 1." - ret += "stress %d\n" % fp_params["stress"] - #paras for deepks - if "out_descriptor" in fp_params: - assert(fp_params["out_descriptor"] == 0 or fp_params["out_descriptor"] == 1), "'out_descriptor' should be either 0 or 1." - ret += "out_descriptor %d\n" % fp_params["out_descriptor"] - if "lmax_descriptor" in fp_params: - assert(fp_params["lmax_descriptor"] >= 0), "'lmax_descriptor' should be a positive integer." - ret += "lmax_descriptor %d\n" % fp_params["lmax_descriptor"] - if "deepks_scf" in fp_params: - assert(fp_params["deepks_scf"] == 0 or fp_params["deepks_scf"] == 1), "'deepks_scf' should be either 0 or 1." - ret += "deepks_scf %d\n" % fp_params["deepks_scf"] - if "model_file" in fp_params: - ret += "model_file %s\n" % fp_params["model_file"] + for key in fp_params: + if key == 'ntype': + assert(fp_params['ntype'] >= 0 and type(fp_params["ntype"]) == int), "'ntype' should be a positive integer." + ret += "ntype %d\n" % fp_params['ntype'] + #ret += "pseudo_dir ./\n" + elif key == "ecutwfc": + assert(fp_params["ecutwfc"] >= 0) , "'ntype' should be non-negative." + ret += "ecutwfc %f\n" % fp_params["ecutwfc"] + elif key == "dr2": + ret += "dr2 %e\n" % fp_params["dr2"] + elif key == "niter": + assert(fp_params['niter'] >= 0 and type(fp_params["niter"])== int), "'niter' should be a positive integer." + ret += "niter %d\n" % fp_params["niter"] + elif key == "basis_type": + assert(fp_params["basis_type"] in ["pw", "lcao", "lcao_in_pw"]) , "'basis_type' must in 'pw', 'lcao' or 'lcao_in_pw'." + ret+= "basis_type %s\n" % fp_params["basis_type"] + elif key == "dft_functional": + ret += "dft_functional %s\n" % fp_params["dft_functional"] + elif key == "gamma_only": + #assert(fp_params["gamma_only"] ==1 ) , "'gamma_only' should be 1. Multi-k algorithm will be supported after the KPT generator is completed." + ret+= "gamma_only %d\n" % fp_params["gamma_only"] + elif key == "mixing_type": + assert(fp_params["mixing_type"] in ["plain", "kerker", "pulay", "pulay-kerker", "broyden"]) + ret += "mixing_type %s\n" % fp_params["mixing_type"] + elif key == "mixing_beta": + assert(fp_params["mixing_beta"] >= 0 and fp_params["mixing_beta"] < 1), "'mixing_beta' should between 0 and 1." + ret += "mixing_beta %f\n" % fp_params["mixing_beta"] + elif key == "symmetry": + assert(fp_params["symmetry"] == 0 or fp_params["symmetry"] == 1), "'symmetry' should be either 0 or 1." + ret += "symmetry %d\n" % fp_params["symmetry"] + elif key == "nbands": + assert(fp_params["nbands"] > 0 and type(fp_params["nbands"]) == int), "'nbands' should be a positive integer." + ret += "nbands %d\n" % fp_params["nbands"] + elif key == "nspin": + assert(fp_params["nspin"] == 1 or fp_params["nspin"] == 2 or fp_params["nspin"] == 4), "'nspin' can anly take 1, 2 or 4" + ret += "nspin %d\n" % fp_params["nspin"] + elif key == "ks_solver": + assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"]), "'ks_sover' should in 'cgx', 'dav', 'lapack', 'genelpa', 'hpseps', 'scalapack_gvx'." + ret += "ks_solver %s\n" % fp_params["ks_solver"] + elif key == "smearing": + assert(fp_params["smearing"] in ["gaussian", "fd", "fixed", "mp", "mp2", "mv"]), "'smearing' should in 'gaussian', 'fd', 'fixed', 'mp', 'mp2', 'mv'. " + ret += "smearing %s\n" % fp_params["smearing"] + elif key == "sigma": + assert(fp_params["sigma"] >= 0), "'sigma' should be non-negative." + ret += "sigma %f\n" % fp_params["sigma"] + elif key == "force": + assert(fp_params["force"] == 0 or fp_params["force"] == 1), "'force' should be either 0 or 1." + ret += "force %d\n" % fp_params["force"] + elif key == "stress": + assert(fp_params["stress"] == 0 or fp_params["stress"] == 1), "'stress' should be either 0 or 1." + ret += "stress %d\n" % fp_params["stress"] + #paras for deepks + elif key == "deepks_out_labels": + assert(fp_params["deepks_out_labels"] == 0 or fp_params["deepks_out_labels"] == 1), "'deepks_out_labels' should be either 0 or 1." + ret += "deepks_out_labels %d\n" % fp_params["deepks_out_labels"] + elif key == "deepks_descriptor_lmax": + assert(fp_params["deepks_descriptor_lmax"] >= 0), "'deepks_descriptor_lmax' should be a positive integer." + ret += "deepks_descriptor_lmax %d\n" % fp_params["deepks_descriptor_lmax"] + elif key == "deepks_scf": + assert(fp_params["deepks_scf"] == 0 or fp_params["deepks_scf"] == 1), "'deepks_scf' should be either 0 or 1." + ret += "deepks_scf %d\n" % fp_params["deepks_scf"] + elif key == "deepks_model": + ret += "deepks_model %s\n" % fp_params["deepks_model"] + else: + ret += "%s %s\n" % (key, str(fp_params[key])) return ret -def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params = None): +def make_abacus_scf_stru(sys_data, fp_pp_files, fp_orb_files = None, fp_dpks_descriptor = None, fp_params = None): atom_names = sys_data['atom_names'] atom_numbs = sys_data['atom_numbs'] assert(len(atom_names) == len(fp_pp_files)), "the number of pp_files must be equal to the number of atom types. " @@ -127,15 +131,15 @@ def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params = None): natom_tot += 1 assert(natom_tot == sum(atom_numbs)) - if fp_params is not None and "basis_type" in fp_params and fp_params["basis_type"]=="lcao": + if fp_orb_files is not None: ret +="\nNUMERICAL_ORBITAL\n" - assert(len(fp_params["orb_files"])==len(atom_names)) + assert(len(fp_orb_files)==len(atom_names)) for iatom in range(len(atom_names)): - ret += fp_params["orb_files"][iatom] +"\n" + ret += fp_orb_files[iatom] +"\n" - if fp_params is not None and "deepks_scf" in fp_params and fp_params["out_descriptor"]==1: + if fp_dpks_descriptor is not None: ret +="\nNUMERICAL_DESCRIPTOR\n" - ret +=fp_params["proj_file"][0]+"\n" + ret +="%s\n"%fp_dpks_descriptor return ret @@ -199,13 +203,29 @@ def get_natoms_from_stru(geometry_inlines): atom_numbs.append(int(geometry_inlines[iline+2].split()[0])) iline += 3+atom_numbs[-1] return atom_names, atom_numbs + +def get_additional_from_STRU(geometry_inlines, nele): + dpks_descriptor_kw = "NUMERICAL_DESCRIPTOR" + orb_file_kw = "NUMERICAL_ORBITAL" + dpks_descriptor = None + orb_file = None + for iline in range(len(geometry_inlines)): + if len(geometry_inlines[iline]) > 0: + if orb_file_kw == geometry_inlines[iline].split()[0]: + orb_file = [] + for iele in range(nele): + orb_file.append(geometry_inlines[iline + iele + 1].rstrip()) + if dpks_descriptor_kw == geometry_inlines[iline].split()[0]: + dpks_descriptor = geometry_inlines[iline + 1].rstrip() + return orb_file, dpks_descriptor + def get_abacus_STRU(STRU, INPUT = None, n_ele = None): # read in geometry from STRU file. n_ele is the number of elements. # Either n_ele or INPUT should be provided. with open(STRU, 'r') as fp: geometry_inlines = fp.read().split('\n') for iline, line in enumerate(geometry_inlines): - if line.split() == []: + if line.split() == [] or len(line) == 0: del geometry_inlines[iline] geometry_inlines.append("") celldm, cell = get_cell(geometry_inlines) @@ -223,6 +243,7 @@ def get_abacus_STRU(STRU, INPUT = None, n_ele = None): inlines = ["ntype %d" %len(atom_numbs)] atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) masses, pp_files = get_mass_from_STRU(geometry_inlines, inlines, atom_names) + orb_files, dpks_descriptor = get_additional_from_STRU(geometry_inlines, len(masses)) data = {} data['atom_names'] = atom_names data['atom_numbs'] = natoms @@ -231,6 +252,8 @@ def get_abacus_STRU(STRU, INPUT = None, n_ele = None): data['coords'] = coords data['atom_masses'] = masses # Notice that this key is not defined in dpdata system. data['pp_files'] = pp_files + data['orb_files'] = orb_files + data['dpks_descriptor'] = dpks_descriptor return data def make_supercell_abacus(from_struct, super_cell): diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py index d43b019a7..dc7a91d3b 100644 --- a/dpgen/generator/run.py +++ b/dpgen/generator/run.py @@ -2190,6 +2190,44 @@ def sys_link_fp_vasp_pp (iter_index, os.symlink(os.path.join('..', 'POTCAR.%s' % ii), 'POTCAR') os.chdir(cwd) +def _link_fp_abacus_orb_descript (iter_index, + jdata) : + # assume lcao orbital files, numerical descrptors and model for dpks are all in fp_pp_path. + fp_pp_path = jdata['fp_pp_path'] + + fp_orb_files = jdata['fp_orb_files'] + assert(os.path.exists(fp_pp_path)) + fp_dpks_descriptor = None + fp_dpks_model = None + if "fp_dpks_descriptor" in jdata: + fp_dpks_descriptor = jdata["fp_dpks_descriptor"] + if "user_fp_params" in jdata: + if "deepks_model" in jdata["user_fp_params"]: + fp_dpks_model = jdata["user_fp_params"]["deepks_model"] + + fp_pp_path = os.path.abspath(fp_pp_path) + + iter_name = make_iter_name(iter_index) + work_path = os.path.join(iter_name, fp_name) + + fp_tasks = glob.glob(os.path.join(work_path, 'task.*')) + fp_tasks.sort() + if len(fp_tasks) == 0 : + return + cwd = os.getcwd() + for ii in fp_tasks: + os.chdir(ii) + for jj in fp_orb_files: + orb_file = os.path.join(fp_pp_path, jj) + os.symlink(orb_file, jj) + if fp_dpks_descriptor is not None: + descrptor = os.path.join(fp_pp_path, fp_dpks_descriptor) + os.symlink(descrptor, fp_dpks_descriptor) + if fp_dpks_model is not None: + dpks_model = os.path.join(fp_pp_path, fp_dpks_model) + os.symlink(dpks_model, fp_dpks_model) + os.chdir(cwd) + def _make_fp_vasp_configs(iter_index, jdata): fp_task_max = jdata['fp_task_max'] @@ -2288,8 +2326,20 @@ def make_fp_abacus_scf(iter_index, iter_name = make_iter_name(iter_index) work_path = os.path.join(iter_name, fp_name) fp_pp_files = jdata['fp_pp_files'] + fp_orb_files = None + fp_dpks_descriptor = None + assert('user_fp_params' in jdata.keys()) if 'user_fp_params' in jdata.keys() : fp_params = jdata['user_fp_params'] + # for lcao + if 'basis_type' in fp_params: + if fp_params['basis_type'] == 'lcao': + assert('fp_orb_files' in jdata and type(jdata['fp_orb_files']) == list and len(jdata['fp_orb_files']) == len(fp_pp_files)) + fp_orb_files = jdata['fp_orb_files'] + if 'deepks_out_labels' in fp_params: + if fp_params['deepks_out_labels'] == 1: + assert('fp_dpks_descriptor' in jdata and type(jdata['fp_dpks_descriptor']) == str) + fp_dpks_descriptor = jdata['fp_dpks_descriptor'] #user_input = True else: raise RuntimeError("Key 'user_fp_params' and its value have to be specified in parameter json file.") @@ -2305,13 +2355,16 @@ def make_fp_abacus_scf(iter_index, ret_kpt = make_abacus_scf_kpt(fp_params) with open("KPT", "w") as fp: fp.write(ret_kpt) - ret_stru = make_abacus_scf_stru(sys_data, fp_pp_files, fp_params) + ret_stru = make_abacus_scf_stru(sys_data, fp_pp_files, fp_orb_files, fp_dpks_descriptor, fp_params) with open("STRU", "w") as fp: fp.write(ret_stru) os.chdir(cwd) # link pp files _link_fp_vasp_pp(iter_index, jdata) + if 'basis_type' in fp_params: + if fp_params['basis_type'] == 'lcao': + _link_fp_abacus_orb_descript(iter_index, jdata) def make_fp_siesta(iter_index, @@ -2621,6 +2674,13 @@ def run_fp (iter_index, run_fp_inner(iter_index, jdata, mdata, forward_files, backward_files, _qe_check_fin, log_file = 'output') elif fp_style == "abacus/scf": forward_files = ["INPUT", "STRU", "KPT"] + fp_pp_files + if "fp_orb_files" in jdata: + forward_files += jdata["fp_orb_files"] + if "fp_dpks_descriptor" in jdata: + forward_files.append(jdata["fp_dpks_descriptor"]) + if "user_fp_params" in jdata: + if "deepks_model" in jdata["user_fp_params"]: + forward_files.append(jdata["user_fp_params"]["deepks_model"]) backward_files = ["output", "OUT.ABACUS"] run_fp_inner(iter_index, jdata, mdata, forward_files, backward_files, _abacus_scf_check_fin, log_file = 'output') elif fp_style == "siesta": diff --git a/examples/init/abacus/CuW.json b/examples/init/abacus/CuW.json index bfa0b8dba..9abd406ce 100644 --- a/examples/init/abacus/CuW.json +++ b/examples/init/abacus/CuW.json @@ -16,10 +16,16 @@ "Cu_ONCV_PBE-1.0.upf", "W_ONCV_PBE-1.0.upf" ], + "orb_files":[ + "Cu_gga_9au_60Ry_4s2p2d1f.orb", + "W_gga_10au_60Ry_4s2p2d2f.orb" + ], "relax_incar": "INPUT", "relax_kpt": "KPT", "md_kpt": "KPT", "md_incar": "INPUT.md", + "dpks_descriptor": "jle.orb", + "dpks_model": "model.ptg", "scale": [ 0.99 ], diff --git a/examples/init/abacus/INPUT b/examples/init/abacus/INPUT index e6fce1bcf..5087da7c5 100644 --- a/examples/init/abacus/INPUT +++ b/examples/init/abacus/INPUT @@ -1,19 +1,16 @@ INPUT_PARAMETERS calculation relax -atom_file STRU -kpoint_file KPT pseudo_dir ./ ntype 2 symmetry 1 ecutwfc 90 -npool 4 -charge_extrap second-order mixing_type pulay mixing_beta 0.4 -dr2 1e-6 -nstep 3 + force_thr_ev 0.02 -move_method cg -out_stru 0 +relax_method cg + +basis_type lcao +deepks_model model.ptg diff --git a/examples/init/abacus/INPUT.md b/examples/init/abacus/INPUT.md index f9d59da2b..33533afe3 100644 --- a/examples/init/abacus/INPUT.md +++ b/examples/init/abacus/INPUT.md @@ -1,19 +1,17 @@ INPUT_PARAMETERS calculation md -atom_file STRU -kpoint_file KPT pseudo_dir ./ ntype 2 symmetry 1 ecutwfc 90 - -npool 4 -charge_extrap second-order +scf_thr 1e-2 mixing_type pulay mixing_beta 0.4 -dr2 1e-6 -nstep 1 -force_thr_ev 0.02 -move_method cg -out_stru 0 +basis_type lcao +md_nstep 3 +cal_stress 1 +deepks_model model.ptg + +md_tfirst 10 +md_tfreq 0.1 diff --git a/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/machine.json b/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/machine.json new file mode 100644 index 000000000..ee4d2f305 --- /dev/null +++ b/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/machine.json @@ -0,0 +1,75 @@ +{ + "api_version": "1.0", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags":["#SBATCH --mem=32G"], + "strategy": {"if_cuda_multi_devices": true}, + "para_deg": 3, + "source_list": ["/home/user1234/deepmd.1.2.4.env"] + } + } + ], + "model_devi":[ + { + "command": "lmp", + "machine":{ + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": ["/home/user1234/deepmd.1.2.4.env"] + } + } + ], + "fp":[ + { + "command": "ABACUS.mpi", + "machine":{ + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": ["~/abacus.env"] + } + } + ] + } \ No newline at end of file diff --git a/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/param.json b/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/param.json new file mode 100644 index 000000000..a578b4a64 --- /dev/null +++ b/examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/param.json @@ -0,0 +1,152 @@ +{ + "type_map": ["H", "C"], + "mass_map": [1.0, 12.0], + + "_comment": "initial data set for Training and the number of frames in each training batch", + "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", + "init_data_sys": [ + "abacus_init_data" + ], + "init_batch_size": [ + 8 + ], + + "_comment": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8 + ], + + "_comment": " 00.train ", + "numb_models": 4, + + "default_training_param": { + "model": { + "type_map": ["H","C"], + "descriptor": { + "type": "se_a", + "sel": [16,4], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [10,20,40], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [120,120,120], + "resnet_dt": true, + "coord_norm": true, + "type_fitting_net": false, + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "decay_rate": 0.95 + }, + "training": { + "set_prefix": "set", + "numb_steps": 2000, + "batch_size": 1, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "numb_test": 4, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment": "that's all" + } + }, + + "_comment": " 01.model_devi ", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_e_trust_lo": 1e-3, + "model_devi_e_trust_hi": 1e-1, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 150 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 9000, + "ensemble": "nvt", + "_idx": "01" + } + ], + + "_comment": " 02.fp ", + "fp_style": "abacus/scf", + "shuffle_poscar": false, + "fp_task_max": 50, + "fp_task_min": 8, + "fp_pp_path": "./", + "fp_pp_files": [ "H_ONCV_PBE-1.0.upf","C_ONCV_PBE-1.0.upf"], + "fp_orb_files": ["H_gga_8au_60Ry_2s1p.orb", "C_gga_8au_60Ry_2s2p1d.orb"], + "fp_dpks_descriptor": "jle.orb", + "user_fp_params":{ + "ntype": 2, + "cal_force": 1, + "cal_stress": 1, + "deepks_model": "model.ptg", + "deepks_out_labels": 1, + "basis_type": "lcao", + "gamma_only": 1, + "ecutwfc": 80, + "mixing_type": "pulay", + "mixing_beta": 0.4, + "symmetry": 1, + "nbands": 5, + "nspin": 1, + "smearing_method": "fixed" + } +} diff --git a/examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json b/examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json index 292d05e3b..ee4d2f305 100644 --- a/examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json +++ b/examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json @@ -1,88 +1,75 @@ { - "train":[ - { - "machine":{ - "machine_type": "slurm", - "host_name": "localhost", - "port": 22, - "username": "", - "work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus" + "api_version": "1.0", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } }, - - "resources":{ - "numb_node": 1, - "numb_gpu": 1, - "task_per_node": 1, - "partition": "", - "exclude_list": [], - "mem_limit": 0, - "source_list": ["/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh"], - "module_list": [], - "time_limit": "23:0:0", - "account":"", - "qos": "" - }, - "python_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_dpgen_interface/4_deepmd-kit/dpmd_install/bin/python" - } + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags":["#SBATCH --mem=32G"], + "strategy": {"if_cuda_multi_devices": true}, + "para_deg": 3, + "source_list": ["/home/user1234/deepmd.1.2.4.env"] + } + } ], -"model_devi": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "localhost", - "port": 22, - "username": "", - "work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus" - }, - "resources": { - "num_node": 1, - "num_gpu": 0, - "task_per_node": 2, - "partition": "cn-large", - "exclude_list": [], - "mem_limit": 0, - "source_list": ["/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh"], - "module_list": [], - "time_limit": "14:00:00", - "account": "", - "qos": "", - "allow_failure":true - }, - "command": "mpirun -n 2 lmp", - "group_size": 6 - } -], -"fp": [ - { + "model_devi":[ + { + "command": "lmp", "machine":{ - "machine_type": "slurm", - "hostname": "localhost", - "port": 22, - "username": "", - "work_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus" + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } }, "resources": { - "cvasp": false, - "numb_node": 1, - "partition": "cn-large", - "task_per_node": 4, - - "numb_gpu": 0, - "exclude_list": [], - "with_mpi": false, - "mem_limit": 0, - "source_list":[ - "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/env.sh" - ], - "module_list":[], - "time_limit": "48:0:0", - "account": "", - "qos": "", - "_comment": "that's all" + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": ["/home/user1234/deepmd.1.2.4.env"] + } + } + ], + "fp":[ + { + "command": "ABACUS.mpi", + "machine":{ + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } }, - "command": "mpirun -np 4 ABACUS.mpi.2.1.0", - "group_size": 150 - } - -] -} + "resources": { + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": ["~/abacus.env"] + } + } + ] + } \ No newline at end of file diff --git a/examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json b/examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json index 916a0c9fb..a5e684d3d 100644 --- a/examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json +++ b/examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json @@ -67,22 +67,19 @@ "decay_rate": 0.95 }, "training": { - "systems": [], - "set_prefix": "set", - "stop_batch": 36000, - "batch_size": 1, - "seed": 1, - "_comment": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" + "set_prefix": "set", + "numb_steps": 2000, + "batch_size": 1, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "numb_test": 4, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment": "that's all" } }, diff --git a/requirements.txt b/requirements.txt index ab3889a32..2e4600c67 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,3 +3,4 @@ monty==2.0.4 ase==3.17.0 paramiko==2.6.0 custodian==2019.2.10 +dpdata==0.2.6 diff --git a/setup.py b/setup.py index e051389bf..3a86a8bd7 100755 --- a/setup.py +++ b/setup.py @@ -17,7 +17,7 @@ with open(path.join('dpgen', '_date.py'), 'w') as fp : fp.write('date = \'%s\'' % today) -install_requires=['numpy>=1.14.3', 'dpdata>=0.2.4', 'pymatgen>=2019.1.13', 'ase', 'monty>2.0.0', 'paramiko', 'custodian','GromacsWrapper>=0.8.0', 'dpdispatcher>=0.3.11'] +install_requires=['numpy>=1.14.3', 'dpdata>=0.2.6', 'pymatgen>=2019.1.13', 'ase', 'monty>2.0.0', 'paramiko', 'custodian','GromacsWrapper>=0.8.0', 'dpdispatcher>=0.3.11'] setuptools.setup( name=NAME, diff --git a/tests/data/abacus.out/box.raw b/tests/data/abacus.out/box.raw index 113faa567..39b35371c 100644 --- a/tests/data/abacus.out/box.raw +++ b/tests/data/abacus.out/box.raw @@ -1,9 +1,8 @@ -9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 -9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 -9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794601733276e+00 -9.706914375293798969e+00 0.000000000000000000e+00 0.000000000000000000e+00 -2.813826031966266683e-01 9.684068716817010980e+00 0.000000000000000000e+00 1.582462665518686029e-01 -1.638176684236652414e-01 9.582973862484221783e+00 -9.706914375293798969e+00 0.000000000000000000e+00 0.000000000000000000e+00 -2.813826031966266683e-01 9.684068716817010980e+00 0.000000000000000000e+00 1.582462665518686029e-01 -1.638176684236652414e-01 9.582973862484221783e+00 -9.706914375293798969e+00 0.000000000000000000e+00 0.000000000000000000e+00 -2.813826031966266683e-01 9.684068716817010980e+00 0.000000000000000000e+00 1.582462665518686029e-01 -1.638176684236652414e-01 9.582973862484221783e+00 -9.270692588887365915e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.282384570089394570e-02 9.562095206948105997e+00 0.000000000000000000e+00 1.695607748098341694e-01 -3.003052827686297777e-02 9.586097959903160159e+00 -9.270692588887365915e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.282384570089394570e-02 9.562095206948105997e+00 0.000000000000000000e+00 1.695607748098341694e-01 -3.003052827686297777e-02 9.586097959903160159e+00 -9.270692588887365915e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.282384570089394570e-02 9.562095206948105997e+00 0.000000000000000000e+00 1.695607748098341694e-01 -3.003052827686297777e-02 9.586097959903160159e+00 +9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 +9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 +9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 +9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 9.500003794602772444e+00 +9.679120507628656611e+00 0.000000000000000000e+00 0.000000000000000000e+00 6.483195033755180525e-02 9.384493548173903577e+00 0.000000000000000000e+00 2.108941915338771733e-01 -3.198873651008774660e-02 9.460865082843536555e+00 +9.679120507628656611e+00 0.000000000000000000e+00 0.000000000000000000e+00 6.483195033755180525e-02 9.384493548173903577e+00 0.000000000000000000e+00 2.108941915338771733e-01 -3.198873651008774660e-02 9.460865082843536555e+00 +9.679120507628656611e+00 0.000000000000000000e+00 0.000000000000000000e+00 6.483195033755180525e-02 9.384493548173903577e+00 0.000000000000000000e+00 2.108941915338771733e-01 -3.198873651008774660e-02 9.460865082843536555e+00 +9.679120507628656611e+00 0.000000000000000000e+00 0.000000000000000000e+00 6.483195033755180525e-02 9.384493548173903577e+00 0.000000000000000000e+00 2.108941915338771733e-01 -3.198873651008774660e-02 9.460865082843536555e+00 diff --git a/tests/data/abacus.out/coord.raw b/tests/data/abacus.out/coord.raw index e7cdddd7b..75fa25209 100644 --- a/tests/data/abacus.out/coord.raw +++ b/tests/data/abacus.out/coord.raw @@ -1,9 +1,8 @@ -5.097445536080835282e+00 3.891296554306815647e+00 3.462257382935012284e+00 3.796296516360798901e+00 4.557085320243889015e+00 4.168354664972580892e+00 5.223520086438995236e+00 5.328267128278273645e+00 4.206763180314156081e+00 5.007081499986584028e+00 3.977917588905994339e+00 5.081172029580683258e+00 4.779784409196943251e+00 4.440311273600644704e+00 4.230028689607135739e+00 -5.103858038642191453e+00 3.880191049870926445e+00 3.446696376719454946e+00 3.775406008016469528e+00 4.559602821249458593e+00 4.167053164452720893e+00 5.232839590161499466e+00 5.347001135761228596e+00 4.206288180124425402e+00 5.011717501838350408e+00 3.968455585126571261e+00 5.098652036562749679e+00 4.779831909215916497e+00 4.440254273577877164e+00 4.230019189603340557e+00 -5.119884545043685620e+00 3.852460538794483913e+00 3.407831861195739442e+00 3.723554987305532915e+00 4.565872823753895915e+00 4.163823163162556185e+00 5.256010099416533521e+00 5.393560654358571682e+00 4.205100679650100481e+00 5.023279006456379925e+00 3.944876575708369693e+00 5.142219053964794284e+00 4.779936409257657282e+00 4.440121273524752610e+00 4.229990689591956787e+00 -5.096427141274351591e+00 3.892434814655956199e+00 3.461810975926975509e+00 3.799155116014967248e+00 4.554677025268077273e+00 4.165565410440091654e+00 5.223901104614204094e+00 5.330327801876574512e+00 4.211142034130066492e+00 5.005414683285621003e+00 3.981651944054248382e+00 5.086652109180486825e+00 4.779872942327282992e+00 4.438974334583333459e+00 4.227730161886026572e+00 -5.103261184602785328e+00 3.880885452800337809e+00 3.445730745785726690e+00 3.777497491778390781e+00 4.557324506181583246e+00 4.164214211125480958e+00 5.232832268549433508e+00 5.348378395685436715e+00 4.210605387593767013e+00 5.009806980159292600e+00 3.972575732728341968e+00 5.103211488014860464e+00 4.780001031169360814e+00 4.438972368771311849e+00 4.227845157572376777e+00 -5.120317329672263718e+00 3.852138687647257420e+00 3.405769744779167496e+00 3.723931089270374528e+00 4.563947804773200723e+00 4.160850587299749215e+00 5.255117341672209008e+00 5.393433560233562574e+00 4.209187107462120103e+00 5.020812710907808452e+00 3.949719756157049844e+00 5.144657849970104557e+00 4.780287402210577241e+00 4.438957933990210769e+00 4.228123063814388516e+00 -5.092902177223409765e+00 3.892432334041243447e+00 3.458357388798343202e+00 3.803614275703672387e+00 4.550054118936396108e+00 4.167057610973984083e+00 5.219810487586725500e+00 5.333212587629732937e+00 4.208594173434244468e+00 5.008144400245305050e+00 3.980022803515795626e+00 5.084715596479592925e+00 4.787731765421213481e+00 4.439473528109648903e+00 4.223443039174134661e+00 -5.100124249224302631e+00 3.880379635300070795e+00 3.441466684192993952e+00 3.782477175789192625e+00 4.552601510199592028e+00 4.165821004337156630e+00 5.229095946058231803e+00 5.351937001907162816e+00 4.208009421458690724e+00 5.012598716327302917e+00 3.971175194607369896e+00 5.100829827150191065e+00 4.787754168232674523e+00 4.439444151121876736e+00 4.223663519427212520e+00 -5.118183394455877000e+00 3.850590682409233079e+00 3.399700055381695840e+00 3.730032485145450494e+00 4.558979655559638466e+00 4.162695936402228014e+00 5.252297961232436307e+00 5.398442395905188818e+00 4.206437301393266104e+00 5.023908229323359897e+00 3.948874057084713840e+00 5.141254402247102284e+00 4.787753781670383901e+00 4.439366062742222674e+00 4.224171582619086429e+00 +5.113541513666988614e+00 3.863321621856395272e+00 3.422849405750413077e+00 3.744792403700195393e+00 4.563437071260724842e+00 4.165241540969359946e+00 5.246389149540494401e+00 5.374789016472041325e+00 4.205651317203156658e+00 5.018535901976148850e+00 3.954367808247492011e+00 5.125120084596087366e+00 4.780862619202477681e+00 4.438958262478904793e+00 4.229719203879755085e+00 +5.120025271365844510e+00 3.856579371274426293e+00 3.414705952782826515e+00 3.737785044340109497e+00 4.567585642723551942e+00 4.159519054131839866e+00 5.250084679248121944e+00 5.385581123343794019e+00 4.200962896678091418e+00 5.021803418638587146e+00 3.949167678661201553e+00 5.132094095892159480e+00 4.780322156232239550e+00 4.438706615138793055e+00 4.230691143249183384e+00 +5.130668193311530345e+00 3.842257606605119058e+00 3.395862296092527544e+00 3.714827908695999437e+00 4.573237572833039444e+00 4.153228609383069703e+00 5.260288809266615573e+00 5.408911614680068425e+00 4.196383384031074470e+00 5.028390217665488215e+00 3.936998920621842313e+00 5.152530157847158954e+00 4.779946425252074249e+00 4.438497469932701556e+00 4.231469808740525806e+00 +5.139819240552561119e+00 3.829166724568353608e+00 3.378433997779851872e+00 3.691026689252517201e+00 4.577843098496067853e+00 4.148427493258955323e+00 5.270227718944992645e+00 5.430404213260533908e+00 4.193244443684692513e+00 5.034444098407153234e+00 3.925351014385712656e+00 5.173263307232290664e+00 4.779833739227024481e+00 4.438383380785650978e+00 4.231858841799698290e+00 +5.113130842373807994e+00 3.868695650279761811e+00 3.415487571001170508e+00 3.744651239412133403e+00 4.563580662541786737e+00 4.164111062857862144e+00 5.240406961795859964e+00 5.372954889528233302e+00 4.205693456774174166e+00 5.018637881428192671e+00 3.954691356908634603e+00 5.129125907828851361e+00 4.777789213993123951e+00 4.437703393219351256e+00 4.232924724680167117e+00 +5.119291532870520633e+00 3.862413940254995293e+00 3.408309249042009270e+00 3.737114389353814126e+00 4.567707592816605100e+00 4.158438791080364183e+00 5.244273868122562909e+00 5.384140787221159741e+00 4.201093323698148474e+00 5.021865322738613635e+00 3.949477760356338241e+00 5.135847808612812315e+00 4.777309286134913791e+00 4.437382988427210684e+00 4.233825195674564945e+00 +5.129194981686882038e+00 3.849057223489113166e+00 3.391777933906729103e+00 3.712887216905144339e+00 4.573278252293058621e+00 4.152308704082664725e+00 5.254885805290236078e+00 5.408420515728852074e+00 4.196773594748246516e+00 5.028351580134470034e+00 3.937225159892942195e+00 5.155667666999540266e+00 4.777076424627810347e+00 4.437027035111054118e+00 4.234426241708828975e+00 +5.137770373040658534e+00 3.836513195982588886e+00 3.376448677962978095e+00 3.687820383509105238e+00 4.577748259206027015e+00 4.147750333825657165e+00 5.265244251783798290e+00 5.430908726685756527e+00 4.193982473292017232e+00 5.034322955639100705e+00 3.925327005711702455e+00 5.175896964276449630e+00 4.777089989406817061e+00 4.436815864047960467e+00 4.234631824221919416e+00 diff --git a/tests/data/abacus.out/energy.raw b/tests/data/abacus.out/energy.raw index d6e8aa5d7..bfa98ed00 100644 --- a/tests/data/abacus.out/energy.raw +++ b/tests/data/abacus.out/energy.raw @@ -1,9 +1,8 @@ --2.191299378191779965e+02 --2.194405277004599952e+02 --2.198624336150280101e+02 --2.191326527145239993e+02 --2.194421046524030032e+02 --2.198623721410370138e+02 --2.191187282189270036e+02 --2.194341917153120107e+02 --2.198612731451000002e+02 +-2.194176123439999913e+02 +-2.194929689141850133e+02 +-2.196084128243170142e+02 +-2.196339131271809890e+02 +-2.194202173360000074e+02 +-2.194938055581540084e+02 +-2.196077839102829898e+02 +-2.196330220266449942e+02 diff --git a/tests/data/abacus.out/force.raw b/tests/data/abacus.out/force.raw index 4144adc07..0cb5a096b 100644 --- a/tests/data/abacus.out/force.raw +++ b/tests/data/abacus.out/force.raw @@ -1,9 +1,8 @@ -1.340516999999999959e+00 -2.319939999999999891e+00 -3.252981999999999818e+00 -4.366520999999999653e+00 5.253839999999999621e-01 -2.713240000000000096e-01 1.946277000000000035e+00 3.914839999999999876e+00 -1.002760000000000040e-01 9.686479999999999535e-01 -1.975710000000000077e+00 3.652965000000000018e+00 1.110799999999999982e-01 -1.445730000000000071e-01 -2.838299999999999851e-02 -1.004871000000000070e+00 -1.739881000000000011e+00 -2.441946999999999868e+00 -3.252618000000000009e+00 3.932160000000000100e-01 -2.014640000000000042e-01 1.449497000000000035e+00 2.920978999999999992e+00 -7.423100000000000531e-02 7.239849999999999897e-01 -1.478039000000000103e+00 2.737074999999999925e+00 7.426499999999999768e-02 -9.627499999999999947e-02 -1.943299999999999889e-02 -3.081909999999999927e-01 -5.357279999999999820e-01 -7.577249999999999819e-01 -9.752370000000000205e-01 1.223179999999999962e-01 -5.883499999999999841e-02 4.313279999999999892e-01 8.821980000000000377e-01 -2.097399999999999959e-02 2.183859999999999968e-01 -4.492929999999999979e-01 8.426649999999999974e-01 1.733200000000000018e-02 -1.949499999999999844e-02 -5.131000000000000144e-03 -1.427623000000000086e+00 -2.413518999999999970e+00 -3.360831999999999820e+00 -4.528626000000000040e+00 5.543489999999999807e-01 -2.825799999999999979e-01 1.865701999999999972e+00 3.772834000000000021e+00 -1.115990000000000038e-01 9.166830000000000256e-01 -1.897685000000000066e+00 3.461780000000000079e+00 3.186169999999999836e-01 -1.597900000000000015e-02 2.932310000000000194e-01 -1.068959999999999910e+00 -1.799541999999999975e+00 -2.503127999999999798e+00 -3.353024000000000004e+00 4.141170000000000129e-01 -2.095920000000000005e-01 1.397261000000000086e+00 2.832427000000000028e+00 -9.248800000000000077e-02 6.915970000000000173e-01 -1.440531999999999924e+00 2.608916999999999931e+00 1.952059999999999906e-01 -6.470000000000000057e-03 1.962909999999999933e-01 -3.321569999999999800e-01 -5.401329999999999742e-01 -7.446800000000000086e-01 -9.782939999999999969e-01 1.297010000000000107e-01 -6.194899999999999712e-02 4.260439999999999783e-01 8.800499999999999989e-01 -5.013700000000000101e-02 2.190239999999999965e-01 -4.777859999999999885e-01 8.186620000000000008e-01 1.069000000000000072e-03 8.167999999999999913e-03 3.810399999999999898e-02 -1.508321999999999941e+00 -2.517781999999999965e+00 -3.530746999999999858e+00 -4.418461999999999890e+00 5.307359999999999856e-01 -2.590069999999999872e-01 1.940423000000000009e+00 3.914120000000000044e+00 -1.216489999999999932e-01 9.302350000000000341e-01 -1.848592999999999931e+00 3.369225999999999832e+00 3.948200000000000320e-02 -7.847999999999999421e-02 5.421770000000000200e-01 -1.133156999999999970e+00 -1.856662000000000035e+00 -2.608308000000000071e+00 -3.288841000000000125e+00 4.018760000000000110e-01 -1.963060000000000083e-01 1.454909000000000008e+00 2.915560000000000151e+00 -1.033980000000000038e-01 7.166339999999999932e-01 -1.407418999999999976e+00 2.547271999999999981e+00 -1.585999999999999910e-02 -5.335600000000000065e-02 3.607400000000000051e-01 -3.706369999999999942e-01 -5.229000000000000314e-01 -7.455789999999999917e-01 -9.850360000000000227e-01 1.368810000000000027e-01 -6.710800000000000098e-02 4.571290000000000076e-01 8.672569999999999446e-01 -6.185999999999999832e-02 2.617059999999999942e-01 -4.714160000000000017e-01 8.086250000000000382e-01 -1.044360000000000011e-01 -9.821999999999999134e-03 6.592199999999999449e-02 +6.681760905239999548e-01 -1.155967561983000103e+00 -1.620154186473999891e+00 -2.080502119690000207e+00 2.497103336489999992e-01 -1.295823446350000130e-01 9.348012021010000394e-01 1.879024337850000004e+00 -4.843350938899999847e-02 4.774995971179999965e-01 -9.733571309149999795e-01 1.797915441510999912e+00 2.522994699999999902e-05 5.900213989999999586e-04 2.545989869999999906e-04 +4.902549688719999854e-01 -8.603996332259999935e-01 -1.205700903469000052e+00 -1.763823817171999986e+00 1.889546707599999986e-01 -9.843194327899999763e-02 7.252026927829999803e-01 1.420961754764999974e+00 -1.878482660100000076e-02 3.788428604390000065e-01 -7.845533793900000274e-01 1.495612918186999929e+00 1.695232950780000136e-01 3.503658709100000018e-02 -1.726952448380000005e-01 +1.600251149420000019e-01 -3.088749268920000235e-01 -4.309845942409999964e-01 -8.343811928180000503e-01 5.437479820200000202e-02 -2.141280961400000155e-02 2.937467391099999880e-01 5.233057998300000291e-01 2.732362033599999851e-02 1.460526182509999937e-01 -3.256663520390000177e-01 6.880404890289999464e-01 2.345567205150000112e-01 5.686068089900000316e-02 -2.629667055100000095e-01 +-1.014967635109999960e-01 1.250831527160000123e-01 1.800253993350000026e-01 8.654394694999999540e-03 -6.285089338900000377e-02 5.043301099599999809e-02 -5.771566249800000326e-02 -1.984398833290000053e-01 6.496074637099999438e-02 -5.642669293500000155e-02 7.369607476700000548e-02 -2.676083779900000070e-02 2.069847242489999961e-01 6.251154923500000515e-02 -2.686583189019999818e-01 +6.006731840350000295e-01 -1.059740442672999938e+00 -1.418495993187999904e+00 -2.191135947068000078e+00 2.451885403140000030e-01 -1.190902165670000012e-01 9.706092934319999754e-01 1.961304510034000081e+00 -2.998638941900000007e-02 4.691260984799999756e-01 -9.761709706690000488e-01 1.745238499110000063e+00 1.507273711209999867e-01 -1.705816370059999865e-01 -1.776658999359999880e-01 +4.420952958250000120e-01 -8.015875351619999867e-01 -1.052519150428000039e+00 -1.844676097365000045e+00 1.816663955479999870e-01 -8.535898558099999645e-02 7.507074338789999635e-01 1.480714365731000015e+00 9.302213549999999468e-04 3.713432452559999875e-01 -7.909188087580000248e-01 1.452768625602999908e+00 2.805301224060000043e-01 -6.987441735900000450e-02 -3.158207109480000163e-01 +1.486986759820000115e-01 -3.179899281079999751e-01 -3.700184322000000248e-01 -8.545027028670000302e-01 4.119800933300000328e-02 -2.061590459000000198e-03 2.997173780390000042e-01 5.403247622500000347e-01 4.908535374100000265e-02 1.399911739220000007e-01 -3.386418890180000196e-01 6.657504093030000014e-01 2.660954749230000083e-01 7.510904554300000535e-02 -3.427557403859999852e-01 +-8.944999494800000284e-02 7.442795737500000619e-02 1.800067342520000058e-01 3.338775485699999740e-02 -7.984094083499999883e-02 7.354084325800000488e-02 -6.629687001900000376e-02 -2.143503895849999952e-01 8.691687501900000057e-02 -6.278862867499999945e-02 5.975731948900000340e-02 -3.768322513999999845e-02 1.851477387859999935e-01 1.600060535560000052e-01 -3.027812273889999850e-01 diff --git a/tests/data/abacus.out/virial.raw b/tests/data/abacus.out/virial.raw index 81d860769..e73cb6b06 100644 --- a/tests/data/abacus.out/virial.raw +++ b/tests/data/abacus.out/virial.raw @@ -1,9 +1,8 @@ -5.795858174693855780e+00 3.443092965380536302e-02 1.929418518002443822e-02 3.443092965380536302e-02 5.716638835032358479e+00 -2.389685573149830794e-02 1.929418518002443822e-02 -2.389685573149830794e-02 5.617522216398079138e+00 -4.408988076950304702e+00 2.176542487386309843e-02 1.214803211126708540e-02 2.176542487386309843e-02 4.359248625442528002e+00 -1.506503678236161513e-02 1.214803211126708540e-02 -1.506503678236161513e-02 4.296671356642591810e+00 -1.386467678460361785e+00 -6.721258240496656147e-04 -3.665654374793160769e-04 -6.721258240496656147e-04 1.386947691887250755e+00 5.415536098234567707e-04 -3.665654374793160769e-04 5.415536098234567707e-04 1.389181332961759718e+00 -5.920273248601972682e+00 -6.039738868480488271e-02 -5.548276701405261552e-02 -6.039738868480488271e-02 5.605862281032128358e+00 1.215189545474988780e-01 -5.548276701405261552e-02 1.215189545474988780e-01 5.558883535614017823e+00 -4.490640109820734693e+00 -4.527006960785832923e-02 -4.134669356180990796e-02 -4.527006960785832923e-02 4.293001025437428453e+00 7.126623109612076346e-02 -4.134669356180990796e-02 7.126623109612076346e-02 4.248516980437247348e+00 -1.394114722102968162e+00 -1.766924844126081806e-02 -1.462129465140290206e-02 -1.766924844126081806e-02 1.399656251812032570e+00 -1.912491203874137902e-02 -1.462129465140290206e-02 -1.912491203874137902e-02 1.360744660235811310e+00 -5.844498499100296840e+00 -6.853191054575857519e-03 -1.324669162954480450e-01 -6.853191054575857519e-03 5.775330648915621978e+00 2.461468284624128700e-01 -1.324669162954480450e-01 2.461468284624128700e-01 5.611345206312754463e+00 -4.456000939126254501e+00 -1.359924298733263329e-02 -9.024508563996384847e-02 -1.359924298733263329e-02 4.394864279944473040e+00 1.488666274174575976e-01 -9.024508563996384847e-02 1.488666274174575976e-01 4.279539092748385620e+00 -1.432096287462409911e+00 -2.596479489866933624e-02 -1.308794539607722671e-02 -2.596479489866933624e-02 1.380061149718328606e+00 -2.498250948476371872e-02 -1.308794539607722671e-02 -2.498250948476371872e-02 1.354370036932820875e+00 +2.925185435890660823e+00 -1.143066424579545657e-04 8.881725950484575360e-05 -1.143066424579545657e-04 2.926987607980041428e+00 -1.622153345284976810e-04 8.881725950484575360e-05 -1.622153345284976810e-04 2.926977964750569594e+00 +2.436657435753112111e+00 -1.143020376950368636e-02 4.544063554962263218e-02 -1.143020376950368636e-02 2.255249757662518117e+00 -6.082814107967922379e-02 4.544063554962263218e-02 -6.082814107967922379e-02 2.339991196674894525e+00 +1.122805829437958147e+00 4.027865798844964401e-03 5.579882761091184418e-02 4.027865798844964401e-03 8.632917807339579586e-01 -6.449198040758287453e-02 5.579882761091184418e-02 -6.449198040758287453e-02 9.953008144738632046e-01 +-8.627979325430941426e-02 3.478382138386666711e-02 3.502648607774696415e-02 3.478382138386666711e-02 -3.189408991107919311e-01 -2.448769152305691615e-02 3.502648607774696415e-02 -2.448769152305691615e-02 -1.845621096491250612e-01 +3.025236369053594832e+00 6.359114793509076935e-02 5.382261098457663540e-02 6.359114793509076935e-02 2.940675387546062058e+00 -7.889899733201287402e-02 5.382261098457663540e-02 -7.889899733201287402e-02 2.733246715970101715e+00 +2.509450100200702138e+00 3.496063080696146241e-02 8.455888007773477988e-02 3.496063080696146241e-02 2.273669135860442836e+00 -1.139127866385887533e-01 8.455888007773477988e-02 -1.139127866385887533e-01 2.186437923758526747e+00 +1.138305236971204781e+00 1.726041882590492391e-02 6.262916189679723633e-02 1.726041882590492391e-02 8.889569868360537308e-01 -6.779923277145767646e-02 6.262916189679723633e-02 -6.779923277145767646e-02 9.244179456601920863e-01 +-1.187496309838749348e-01 2.448581565458010298e-02 1.754917825266641071e-02 2.448581565458010298e-02 -2.962521051255574966e-01 7.964505747695275681e-03 1.754917825266641071e-02 7.964505747695275681e-03 -1.987105956507752014e-01 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT index c3181c397..f38b2d7d0 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT @@ -1,20 +1,17 @@ INPUT_PARAMETERS calculation md -atom_file STRU -kpoint_file KPT pseudo_dir ./ ntype 2 symmetry 1 ecutwfc 90 -npool 1 - mixing_type pulay mixing_beta 0.4 +basis_type lcao +md_nstep 3 +cal_stress 1 +deepks_model model.ptg -nstep 3 -force_thr_ev 0.02 -#move_method cg -out_stru 0 -stress 1 +md_tfirst 10 +md_tfreq 0.1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT deleted file mode 100644 index 63bd0ed40..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT +++ /dev/null @@ -1,263 +0,0 @@ -INPUT_PARAMETERS -#Parameters (1.General) -suffix ABACUS #the name of main output directory -latname test #the name of lattice name -atom_file STRU #the filename of file containing atom positions -kpoint_file KPT #the name of file containing k points -pseudo_dir .// #the directory containing pseudo files -orbital_dir #the directory containing orbital files -pseudo_type auto #the type pseudo files -pseudo_rcut 15 #cut-off radius for radial integration -renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE -lmaxmax 2 #maximum of l channels used -dft_functional none #exchange correlation functional -calculation md #test; scf; relax; nscf; ienvelope; istate; -ntype 2 #atom species number -nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin -nbands 0 #number of bands -nbands_sto 0 #number of stochastic bands -nbands_istate 5 #number of bands around Fermi level for istate calulation -nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT -symmetry 0 #turn symmetry on or off -set_vel 0 #read velocity from STRU or not -symmetry_prec 1e-05 #accuracy for symmetry -nelec 0 #input number of electrons -tot_magnetization 0 #total magnetization of the system - -#Parameters (2.PW) -ecutwfc 90 ##energy cutoff for wave functions -diago_cg_maxiter 50 #max iteration number for cg -diago_cg_prec 1 #diago_cg_prec -ethr 0.01 #threshold for eigenvalues is cg electron iterations -dr2 1e-09 #charge density error -start_wfc atomic #start wave functions are from 'atomic' or 'file' -start_charge atomic #start charge is from 'atomic' or file -charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA -out_charge 0 #>0 output charge density for selected electron steps -out_potential 0 #output realspace potential -out_wf 0 #output wave functions -out_dos 0 #output energy and dos -out_band 0 #output energy and band structure -restart_save 0 #print to disk every step for restart -restart_load 0 #restart from disk -read_file_dir auto #directory of files for reading -nx 0 #number of points along x axis for FFT grid -ny 0 #number of points along y axis for FFT grid -nz 0 #number of points along z axis for FFT grid -cell_factor 1.2 #used in the construction of the pseudopotential tables - -#Parameters (3.Relaxation) -ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx -niter 40 ##number of electron iterations -force_set 0 #output the force_set or not -nstep 3 #number of ion iteration steps -out_stru 0 #output the structure files after each ion step -force_thr 0.00077787 #force threshold, unit: Ry/Bohr -force_thr_ev 0.02 #force threshold, unit: eV/Angstrom -force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom -cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom -stress_thr 0.01 #stress threshold -press1 0 #target pressure, unit: KBar -press2 0 #target pressure, unit: KBar -press3 0 #target pressure, unit: KBar -bfgs_w1 0.01 #wolfe condition 1 for bfgs -bfgs_w2 0.5 #wolfe condition 2 for bfgs -trust_radius_max 0.8 #maximal trust radius, unit: Bohr -trust_radius_min 1e-05 #minimal trust radius, unit: Bohr -trust_radius_ini 0.5 #initial trust radius, unit: Bohr -stress 1 #calculate the stress or not -fixed_axes None #which axes are fixed -move_method cg #bfgs; sd; cg; cg_bfgs; -out_level m #ie(for electrons); i(for ions); -out_dm 0 #>0 output density matrix -out_descriptor 0 #>0 compute descriptor for deepks -lmax_descriptor 2 #>0 lmax used in descriptor for deepks - -#Parameters (4.LCAO) -basis_type pw #PW; LCAO in pw; LCAO -new_dm 1 #Type of density matrix; 0: old 1: new -search_radius -1 #input search radius (Bohr) -search_pbc 1 #input periodic boundary condition -lcao_ecut 0 #energy cutoff for LCAO -lcao_dk 0.01 #delta k for 1D integration in LCAO -lcao_dr 0.01 #delta r for 1D integration in LCAO -lcao_rmax 30 #max R for 1D two-center integration table -out_hs 0 #output H and S matrix -out_hs2 0 #output H(R) and S(R) matrix -out_r 0 #output r(R) matrix -out_lowf 0 #ouput LCAO wave functions -bx 1 #division of an element grid in FFT grid along x -by 1 #division of an element grid in FFT grid along y -bz 1 #division of an element grid in FFT grid along z - -#Parameters (5.Smearing) -smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv -sigma 0.01 #energy range for smearing - -#Parameters (6.Charge Mixing) -mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden -mixing_beta 0.4 #mixing parameter: 0 means no new charge -mixing_ndim 8 #mixing dimension in pulay -mixing_gg0 0 #mixing parameter in kerker - -#Parameters (7.DOS) -dos_emin_ev -15 #minimal range for dos -dos_emax_ev 15 #maximal range for dos -dos_edelta_ev 0.01 #delta energy for dos -dos_scale 0.01 #scale dos range by -dos_sigma 0.07 #gauss b coefficeinet(default=0.07) - -#Parameters (8.Technique) -gamma_only 0 #gamma only, only used in LCAO basis -diago_proc 8 #number of proc used to diago -npool 1 #number of pools for k points, pw only -mem_saver 0 #memory saver for many k points used -printe 100 #print band energy for selectively ionic steps - -#Parameters (9.SIAO) -selinv_npole 40 #number of selected poles -selinv_temp 2000 #temperature for Fermi-Dirac distribution -selinv_gap 0 #supposed gap in the calculation -selinv_deltae 2 #expected energy range -selinv_mu -1 #chosen mu as Fermi energy -selinv_threshold 0.001 #threshold for calculated electron number -selinv_niter 50 #max number of steps to update mu - -#Parameters (10.Molecular dynamics) -md_mdtype 1 #choose ensemble -md_potential FP #choose potential -md_dt 1 #time step -mnhc 4 #number of Nose-Hoover chains -md_qmass 1 #mass of thermostat -md_tfirst 0 #temperature first -md_tlast 0 #temperature last -md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD -md_mdoutpath mdoutput #output path of md -md_rstmd 0 #whether restart -md_fixtemperature 1 #period to change temperature -md_ediff 0.0001 #parameter for constraining total energy change -md_ediffg 0.001 #parameter for constraining max force change -NVT_tau 0 #parameter for adjust effect of thermostat -NVT_control 1 #choose which thermostat used in NVT ensemble -rcut_lj 8.5 #cutoff radius of LJ potential -epsilon_lj 0.01032 #the value of epsilon for LJ potential -sigma_lj 3.405 #the value of sigma for LJ potential - -#Parameters (11.Efield) -efield 0 #add electric field -edir 1 #add electric field -emaxpos 0.5 #maximal position of efield [0,1) -eopreg 0.1 #where sawlike potential decrease -eamp 0.001 #amplitute of the efield, unit is a.u. -eamp_v 0.05144 #amplitute of the efield, unit is V/A - -#Parameters (12.Test) -out_alllog 0 #output information for each processor, when parallel -nurse 0 #for coders -colour 0 #for coders, make their live colourful -t_in_h 1 #calculate the kinetic energy or not -vl_in_h 1 #calculate the local potential or not -vnl_in_h 1 #calculate the nonlocal potential or not -vh_in_h 1 #calculate the hartree potential or not -vxc_in_h 1 #calculate the xc potential or not -vion_in_h 1 #calculate the local ionic potential or not -test_force 0 #test the force -test_stress 0 #test the force - -#Parameters (13.Other Methods) -mlwf_flag 0 #turn MLWF on or off -opt_epsilon2 0 #calculate the dielectic function -opt_nbands 0 #number of bands for optical calculation - -#Parameters (14.VdW Correction) -vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj -vdw_s6 default #scale parameter of d2/d3_0/d3_bj -vdw_s8 default #scale parameter of d3_0/d3_bj -vdw_a1 default #damping parameter of d3_0/d3_bj -vdw_a2 default #damping parameter of d3_bj -vdw_d 20 #damping parameter of d2 -vdw_abc 0 #third-order term? -vdw_C6_file default #filename of C6 -vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 -vdw_R0_file default #filename of R0 -vdw_R0_unit A #unit of R0, A or Bohr -vdw_model radius #expression model of periodic structure, radius or period -vdw_radius default #radius cutoff for periodic structure -vdw_radius_unit Bohr #unit of radius cutoff for periodic structure -vdw_cn_thr 40 #radius cutoff for cn -vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom -vdw_period 3 3 3 #periods of periodic structure - -#Parameters (15.spectrum) -spectral_type None #the type of the calculated spectrum -spectral_method 0 #0: tddft(linear response) -kernel_type rpa #the kernel type: rpa, tdlda ... -eels_method 0 #0: hilbert_transform method; 1: standard method -absorption_method 0 #0: vasp's method 1: pwscf's method -system bulk #the calculate system -eta 0.05 #eta(Ry) -domega 0.01 #domega(Ry) -nomega 300 #nomega -ecut_chi 1 #the dimension of chi matrix -q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate -q_direction 1 0 0 #the q direction -nq 1 #the total number of qpoints for calculation -out_epsilon 1 #output epsilon or not -out_chi 0 #output chi or not -out_chi0 0 #output chi0 or not -fermi_level 0 #the change of the fermi_level(Ry) -coulomb_cutoff 0 # turn on the coulomb_cutoff or not -kmesh_interpolation 0 #calculting -qcar 0 0 0 #(unit: 2PI/lat0) -ocp 0 #change occupation or not -ocp_set none #set occupation -lcao_box 10 10 10 #the scale for searching the existence of the overlap - mulliken 0 # mulliken charge or not -intrasmear 0 #Eta -shift 0 #shift -metalcalc 0 #metal or not -eps_degauss 0.01 #degauss in calculating epsilon0 -noncolin 0 #using non-collinear-spin -lspinorb 0 #consider the spin-orbit interaction - -#Parameters (17.exx) -exx_hybrid_type no #no, hf, pbe0, hse or opt_orb -exx_hybrid_alpha 0.25 # -exx_hse_omega 0.11 # -exx_separate_loop 1 #0 or 1 -exx_hybrid_step 100 # -exx_lambda 0.3 # -exx_pca_threshold 0 # -exx_c_threshold 0 # -exx_v_threshold 0 # -exx_dm_threshold 0 # -exx_schwarz_threshold0 # -exx_cauchy_threshold0 # -exx_ccp_threshold 1e-08 # -exx_ccp_rmesh_times 10 # -exx_distribute_type htime #htime or kmeans1 or kmeans2 -exx_opt_orb_lmax 0 # -exx_opt_orb_ecut 0 # -exx_opt_orb_tolerence0 # - -#Parameters (17.tddft) -tddft 0 #calculate tddft or not -td_dr2 1e-09 #threshold for electronic iteration of tddft -td_dt 0.02 #time of ion step -td_force_dt 0.02 #time of force change -td_val_elec_01 1 #td_val_elec_01 -td_val_elec_02 1 #td_val_elec_02 -td_val_elec_03 1 #td_val_elec_03 -td_vext 0 #add extern potential or not -td_vext_dire 1 #extern potential direction -td_timescale 0.5 #extern potential td_timescale -td_vexttype 1 #extern potential type -td_vextout 0 #output extern potential or not -td_dipoleout 0 #output dipole or not - -#Parameters (18.berry_wannier) -berry_phase 0 #calculate berry phase or not -gdir 3 #calculate the polarization in the direction of the lattice std::vector -towannier90 0 #use wannier90 code interface or not -nnkpfile seedname.nnkp #the wannier90 code nnkp file name -wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/MD_dump b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/MD_dump new file mode 100644 index 000000000..657704d8a --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/MD_dump @@ -0,0 +1,72 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.500003790419 0.000000000000 0.000000000000 + 0.000000000000 9.500003790419 0.000000000000 + 0.000000000000 0.000000000000 9.500003790419 +VIRIAL (KBAR) + 5.466287376582 -0.000213604563 0.000165972611 + -0.000213604563 5.469655091470 -0.000303131427 + 0.000165972611 -0.000303131427 5.469637071189 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.113541511415 3.863321620155 3.422849404243 0.668176090524 -1.155967561983 -1.620154186474 + 1 H 3.744792402051 4.563437069251 4.165241539135 -2.080502119690 0.249710333649 -0.129582344635 + 2 H 5.246389147230 5.374789014105 4.205651315351 0.934801202101 1.879024337850 -0.048433509389 + 3 H 5.018535899766 3.954367806506 5.125120082339 0.477499597118 -0.973357130915 1.797915441511 + 4 C 4.780862617097 4.438958260524 4.229719202017 0.000025229947 0.000590021399 0.000254598987 + + +MDSTEP: 1 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.500003790419 0.000000000000 0.000000000000 + 0.000000000000 9.500003790419 0.000000000000 + 0.000000000000 0.000000000000 9.500003790419 +VIRIAL (KBAR) + 4.553376212902 -0.021359595809 0.084914812388 + -0.021359595809 4.214380097102 -0.113669409004 + 0.084914812388 -0.113669409004 4.372736231610 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.120025269111 3.856579369576 3.414705951279 0.490254968872 -0.860399633226 -1.205700903469 + 1 H 3.737785042694 4.567585640712 4.159519052300 -1.763823817172 0.188954670760 -0.098431943279 + 2 H 5.250084676936 5.385581120972 4.200962894828 0.725202692783 1.420961754765 -0.018784826601 + 3 H 5.021803416427 3.949167676922 5.132094093632 0.378842860439 -0.784553379390 1.495612918187 + 4 C 4.780322154127 4.438706613184 4.230691141386 0.169523295078 0.035036587091 -0.172695244838 + + +MDSTEP: 2 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.500003790419 0.000000000000 0.000000000000 + 0.000000000000 9.500003790419 0.000000000000 + 0.000000000000 0.000000000000 9.500003790419 +VIRIAL (KBAR) + 2.098184701901 0.007526863665 0.104271142354 + 0.007526863665 1.613231388832 -0.120516017230 + 0.104271142354 -0.120516017230 1.859916370192 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.130668191052 3.842257604913 3.395862294597 0.160025114942 -0.308874926892 -0.430984594241 + 1 H 3.714827907060 4.573237570819 4.153228607554 -0.834381192818 0.054374798202 -0.021412809614 + 2 H 5.260288806950 5.408911612298 4.196383382183 0.293746739110 0.523305799830 0.027323620336 + 3 H 5.028390215451 3.936998918888 5.152530155578 0.146052618251 -0.325666352039 0.688040489029 + 4 C 4.779946423147 4.438497467978 4.231469806877 0.234556720515 0.056860680899 -0.262966705510 + + +MDSTEP: 3 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.500003790419 0.000000000000 0.000000000000 + 0.000000000000 9.500003790419 0.000000000000 + 0.000000000000 0.000000000000 9.500003790419 +VIRIAL (KBAR) + -0.161230853584 0.065000447974 0.065453914936 + 0.065000447974 -0.596004133377 -0.045760093501 + 0.065453914936 -0.045760093501 -0.344890794885 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.139819238289 3.829166722882 3.378433996292 -0.101496763511 0.125083152716 0.180025399335 + 1 H 3.691026687627 4.577843096480 4.148427491432 0.008654394695 -0.062850893389 0.050433010996 + 2 H 5.270227716624 5.430404210869 4.193244441838 -0.057715662498 -0.198439883329 0.064960746371 + 3 H 5.034444096190 3.925351012657 5.173263304954 -0.056426692935 0.073696074767 -0.026760837799 + 4 C 4.779833737122 4.438383378831 4.231858839936 0.206984724249 0.062511549235 -0.268658318902 + + diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD deleted file mode 100644 index ab99de324..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD +++ /dev/null @@ -1,27 +0,0 @@ -ATOMIC_SPECIES -H 1.008 H_ONCV_PBE-1.0.upf -C 12.01 C_ONCV_PBE-1.0.upf - -LATTICE_CONSTANT -1.88972612546 - -LATTICE_VECTORS -9.50000379042 0 0 #latvec1 -0 9.50000379042 0 #latvec2 -0 0 9.50000379042 #latvec3 - -ATOMIC_POSITIONS -Direct - -H #label -0 #magnetism -4 #number of atoms -0.540930980325 0.402075031383 0.353895874486 1 1 1 0 0 0 -0.385586980814 0.481402417362 0.437898545951 1 1 1 0 0 0 -0.556131217776 0.57347946396 0.442495090138 1 1 1 0 0 0 -0.530202220323 0.412321251956 0.546677526283 1 1 1 0 0 0 - -C #label -0 #magnetism -1 #number of atoms -0.503163091902 0.467364749224 0.445258850036 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif deleted file mode 100644 index 779ef9f3b..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.5 -_cell_length_b 9.5 -_cell_length_c 9.5 -_cell_angle_alpha 90 -_cell_angle_beta 90 -_cell_angle_gamma 90 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.536573 0.40961 0.364448 -H 0.39961 0.479693 0.438774 -H 0.549844 0.56087 0.442817 -H 0.527061 0.418728 0.53486 -C 0.503135 0.467401 0.445266 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif deleted file mode 100644 index e09204a1c..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.5 -_cell_length_b 9.5 -_cell_length_c 9.5 -_cell_angle_alpha 90 -_cell_angle_beta 90 -_cell_angle_gamma 90 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.537248 0.408441 0.36281 -H 0.397411 0.479958 0.438637 -H 0.550825 0.562842 0.442767 -H 0.527549 0.417732 0.5367 -C 0.50314 0.467395 0.445265 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif deleted file mode 100644 index 99311ee37..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.5 -_cell_length_b 9.5 -_cell_length_c 9.5 -_cell_angle_alpha 90 -_cell_angle_beta 90 -_cell_angle_gamma 90 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.538935 0.405522 0.358719 -H 0.391953 0.480618 0.438297 -H 0.553264 0.567743 0.442642 -H 0.528766 0.41525 0.541286 -C 0.503151 0.467381 0.445262 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif deleted file mode 100644 index fde6898f6..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.5 -_cell_length_b 9.5 -_cell_length_c 9.5 -_cell_angle_alpha 90 -_cell_angle_beta 90 -_cell_angle_gamma 90 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.540931 0.402075 0.353896 -H 0.385587 0.481402 0.437899 -H 0.556131 0.573479 0.442495 -H 0.530202 0.412321 0.546678 -C 0.503163 0.467365 0.445259 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log index 34c025fe5..684146e69 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log @@ -6,8 +6,8 @@ Website: http://abacus.ustc.edu.cn/ Version: Parallel, in development - Processor Number is 8 - Start Time is Fri Nov 12 18:15:13 2021 + Processor Number is 4 + Start Time is Sun Apr 17 15:10:23 2022 ------------------------------------------------------------------------------------ @@ -18,7 +18,7 @@ orbital_dir = pseudo_type = auto DRANK = 1 - DSIZE = 8 + DSIZE = 4 DCOLOR = 1 GRANK = 1 GSIZE = 1 @@ -52,9 +52,8 @@ READING ATOM TYPE 1 atom label = H - L=0, number of zeta = 1 + L=0, number of zeta = 2 L=1, number of zeta = 1 - L=2, number of zeta = 1 number of atom for this type = 4 start magnetization = FALSE start magnetization = FALSE @@ -63,8 +62,8 @@ READING ATOM TYPE 2 atom label = C - L=0, number of zeta = 1 - L=1, number of zeta = 1 + L=0, number of zeta = 2 + L=1, number of zeta = 2 L=2, number of zeta = 1 number of atom for this type = 1 start magnetization = FALSE @@ -73,12 +72,16 @@ CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). atom x y z mag vx vy vz - tauc_H1 5.09744437597 3.89129339419 3.4622612337 0 0 0 0 - tauc_H2 3.79629251291 4.55708480448 4.16835321433 0 0 0 0 - tauc_H3 5.2235234109 5.32826990334 4.20676661344 0 0 0 0 - tauc_H4 5.00707710352 3.97791420915 5.08117016892 0 0 0 0 - tauc_C1 4.77978417423 4.4403114594 4.23003031273 0 0 0 0 + tauc_H1 5.11354151141 3.86332162016 3.42284940424 0 0 0 0 + tauc_H2 3.74479240205 4.56343706925 4.16524153913 0 0 0 0 + tauc_H3 5.24638914723 5.3747890141 4.20565131535 0 0 0 0 + tauc_H4 5.01853589977 3.95436780651 5.12512008234 0 0 0 0 + tauc_C1 4.7808626171 4.43895826052 4.22971920202 0 0 0 0 + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: H_gga_8au_60Ry_2s1p.orb + orbital file: C_gga_8au_60Ry_2s2p1d.orb Volume (Bohr^3) = 5785.86022047 Volume (A^3) = 857.37500227 @@ -90,7 +93,7 @@ Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) +0.105263115896 +0 +0 +0 +0.105263115896 +0 - +0 +0 +0.105263115896 + +0 -0 +0.105263115896 @@ -117,10 +120,7 @@ Read in pseudopotential file is H_ONCV_PBE-1.0.upf pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = + exchange-correlation functional = PBE nonlocal core correction = 0 valence electrons = 1 lmax = 0 @@ -132,10 +132,7 @@ Read in pseudopotential file is C_ONCV_PBE-1.0.upf pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = + exchange-correlation functional = PBE nonlocal core correction = 0 valence electrons = 4 lmax = 1 @@ -146,7 +143,7 @@ L of projector = 1 L of projector = 1 initial pseudo atomic orbital number = 0 - NLOCAL = 45 + NLOCAL = 33 SETUP THE ELECTRONS NUMBER electron number of element H = 1 @@ -154,8 +151,10 @@ electron number of element C = 4 total electron number of element C = 4 occupied bands = 4 + NLOCAL = 33 NBANDS = 14 - DONE : SETUP UNITCELL Time : 0.086291129759 (SEC) + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.044255124405 (SEC) @@ -190,7 +189,7 @@ KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT 1 0 0 0 2 - DONE : INIT K-POINTS Time : 0.0878850566805 (SEC) + DONE : INIT K-POINTS Time : 0.0458821123466 (SEC) @@ -215,10 +214,10 @@ energy cutoff for wavefunc (unit:Ry) = 90 [fft grid for wave functions] = 120, 120, 120 [fft grid for charge/potential] = 120, 120, 120 - [fft grid division] = 1, 1, 1 - [big fft grid for charge/potential] = 120, 120, 120 - nbxx = 216000 - nrxx = 216000 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 60, 60, 60 + nbxx = 54000 + nrxx = 432000 SETUP PLANE WAVES FOR CHARGE/POTENTIAL number of plane waves = 667317 @@ -230,150 +229,138 @@ PARALLEL PW FOR CHARGE/POTENTIAL PROC COLUMNS(POT) PW - 1 1155 83417 - 2 1157 83415 - 3 1157 83415 - 4 1156 83414 - 5 1156 83414 - 6 1156 83414 - 7 1156 83414 - 8 1156 83414 + 1 2310 166830 + 2 2313 166829 + 3 2313 166829 + 4 2313 166829 --------------- sum ------------------- - 8 9249 667317 + 4 9249 667317 PARALLEL PW FOR WAVE FUNCTIONS PROC COLUMNS(W) PW - 1 289 10449 - 2 289 10453 - 3 290 10452 - 4 287 10451 - 5 293 10449 - 6 290 10448 - 7 288 10448 - 8 287 10449 + 1 575 20899 + 2 580 20900 + 3 578 20898 + 4 580 20902 --------------- sum ------------------- - 8 2313 83599 + 4 2313 83599 SETUP COORDINATES OF PLANE WAVES number of total plane waves = 667317 SETUP COORDINATES OF PLANE WAVES - number of |g| = 2438 + number of |g| = 2450 max |g| = 32.553990643 min |g| = 0 - DONE : INIT PLANEWAVE Time : 0.350971238862 (SEC) + DONE : INIT PLANEWAVE Time : 0.377468010411 (SEC) - npwx = 10449 + DONE : INIT CHARGE Time : 0.403857703321 (SEC) - SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS - H non-local projectors: - projector 1 L=0 - projector 2 L=0 - C non-local projectors: - projector 1 L=0 - projector 2 L=0 - projector 3 L=1 - projector 4 L=1 - TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 - DONE : LOCAL POTENTIAL Time : 0.494807609997 (SEC) + DONE : INIT POTENTIAL Time : 0.408238855191 (SEC) - Init Non-Local PseudoPotential table : - Init Non-Local-Pseudopotential done. - DONE : NON-LOCAL POTENTIAL Time : 0.501984705625 (SEC) - start_pot = atomic - DONE : INIT POTENTIAL Time : 0.639263 (SEC) - Make real space PAO into reciprocal space. - max mesh points in Pseudopotential = 601 - dq(describe PAO in reciprocal space) = 0.01 - max q = 1143 + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - number of pseudo atomic orbitals for H is 0 - number of pseudo atomic orbitals for C is 0 - DONE : INIT BASIS Time : 0.917201 (SEC) - ...............Nose-Hoover Chain parameter initialization............... - Temperature = 0 - Temperature2 = 0 - NHC frequency = 0.00120944 - NHC chain = 4 - Qmass = 1822.89 - ............................................................... - PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - K-point CG iter num Time(Sec) - 1 9.642857 1.320000 - Density error is 0.925917380140 + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 953 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + 4 1 1 801 0.01 8 1 1 + 5 2 0 801 0.01 8 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 - PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - K-point CG iter num Time(Sec) - 1 2.357143 0.370000 + SETUP THE TWO-CENTER INTEGRATION TABLES - Density error is 0.103089655783 + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 33 + trace_loc_col dimension = 33 + nloc = 289 + init_chg = atomic + nloc = 289 + searching radius is (Bohr)) = 18.89 + searching radius unit is (Bohr)) = 1.88973 - PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - K-point CG iter num Time(Sec) - 1 4.500000 0.620000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 1 -------------------------------- - Density error is 0.029305943975 + Density error is 0.369103341079 - PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - K-point CG iter num Time(Sec) - 1 3.928571 0.550000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 2 -------------------------------- - Density error is 0.215036462399 + Density error is 0.143573672298 - PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - K-point CG iter num Time(Sec) - 1 3.285714 0.480000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 3 -------------------------------- - Density error is 0.000079236362 + Density error is 0.0734674541148 - PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - K-point CG iter num Time(Sec) - 1 6.857143 0.890000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 4 -------------------------------- - Density error is 0.000065409462 + Density error is 0.00483129776793 - PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - K-point CG iter num Time(Sec) - 1 3.071429 0.440000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 5 -------------------------------- - Density error is 0.000015159186 + Density error is 0.00175259574578 - PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - K-point CG iter num Time(Sec) - 1 5.214286 0.690000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 6 -------------------------------- - Density error is 0.000000616832 + Density error is 0.000110712686393 - PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- - K-point CG iter num Time(Sec) - 1 4.357143 0.590000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 7 -------------------------------- - Density error is 0.000000158907 + Density error is 6.19582961728e-05 - PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- - K-point CG iter num Time(Sec) - 1 5.857143 0.760000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 8 -------------------------------- - Density error is 0.000000003032 + Density error is 1.8043377224e-06 - PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- - K-point CG iter num Time(Sec) - 1 6.500000 0.840000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 9 -------------------------------- - Density error is 0.000000000145 + Density error is 7.13331944904e-07 - charge density convergence is achieved - final etot is -219.129937819178 eV + LCAO ALGORITHM ------------- MD = 1 ELEC = 10 -------------------------------- + + Density error is 2.6209014458e-08 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 11 -------------------------------- + Density error is 1.41723715595e-08 + LCAO ALGORITHM ------------- MD = 1 ELEC = 12 -------------------------------- + + Density error is 3.11824834896e-10 + + charge density convergence is achieved + final etot is -219.417612344 eV ><><><><><><><><><><><><><><><><><><><><><>< @@ -382,11 +369,11 @@ ><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 +1.340517 -2.319940 -3.252982 - H2 -4.366521 +0.525384 -0.271324 - H3 +1.946277 +3.914840 -0.100276 - H4 +0.968648 -1.975710 +3.652965 - C1 +0.111080 -0.144573 -0.028383 + H1 +0.66817605 -1.1559675 -1.6201541 + H2 -2.080502 +0.24971032 -0.12958234 + H3 +0.93480114 +1.8790242 -0.048433506 + H4 +0.47749957 -0.97335707 +1.7979153 + C1 +2.5229946e-05 +0.00059002136 +0.00025459897 ><><><><><><><><><><><><><><><><><><><><><>< @@ -395,94 +382,75 @@ ><><><><><><><><><><><><><><><><><><><><><>< - +10.830707 +0.064341 +0.036055 - +0.064341 +10.682670 -0.044656 - +0.036055 -0.044656 +10.497451 + +5.466287 -0.000214 +0.000166 + -0.000214 +5.469655 -0.000303 + +0.000166 -0.000303 +5.469637 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +21.340552 Kbar -Virial Term is +21.340552 Kbar -Kenetic Term is +0.000000 Kbar +Virtual Pressure is +5.474968 Kbar +Virial Term is +5.468527 Kbar +Kenetic Term is +0.006441 Kbar + - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 1 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.105748 (Rydberg) - NVT Temperature : +0.000000 (K) - NVT Kinetic energy : +0.000000 (Rydberg) - NVT Potential energy : -16.105748 (Rydberg) - maxForce : +0.007343 - maxStep : +0.039821 - MD_STEP SystemE Conserved DeltaE Temperature - +1 -8.052874 -8.052874 +0.000000 +172.203317 + ><><><><><><><><><><><><><><><><><><><><><>< - PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +53.714286 +6.150000 + MD STRESS (KBAR) - Density error is +0.003432405487 + ><><><><><><><><><><><><><><><><><><><><><>< - PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.340000 + +5.471080 +0.000651 -0.003879 + +0.000651 +5.472481 -0.005115 + -0.003879 -0.005115 +5.481343 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 - Density error is +0.000062275134 + LCAO ALGORITHM ------------- MD = 2 ELEC = 1 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.000000 +0.530000 + Density error is +0.010266517531 - Density error is +0.000015792053 + LCAO ALGORITHM ------------- MD = 2 ELEC = 2 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.142857 +0.450000 + Density error is +0.002497371603 - Density error is +0.000001338459 + LCAO ALGORITHM ------------- MD = 2 ELEC = 3 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.642857 +0.610000 + Density error is +0.001347922782 - Density error is +0.000000192378 + LCAO ALGORITHM ------------- MD = 2 ELEC = 4 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.142857 +0.460000 + Density error is +0.000084761244 - Density error is +0.000000025550 + LCAO ALGORITHM ------------- MD = 2 ELEC = 5 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.714286 +0.640000 + Density error is +0.000012263011 - Density error is +0.000000014039 + LCAO ALGORITHM ------------- MD = 2 ELEC = 6 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.142857 +0.330000 + Density error is +0.000001314208 - Density error is +0.000000005006 + LCAO ALGORITHM ------------- MD = 2 ELEC = 7 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.428571 +0.370000 + Density error is +0.000000452317 - Density error is +0.000000001075 + LCAO ALGORITHM ------------- MD = 2 ELEC = 8 -------------------------------- - PW ALGORITHM --------------- ION=+2 ELEC=+10 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.571429 +0.630000 + Density error is +0.000000076730 - Density error is +0.000000000036 + LCAO ALGORITHM ------------- MD = 2 ELEC = 9 -------------------------------- - charge density convergence is achieved - final etot is -219.440527700460 eV + Density error is +0.000000005728 + LCAO ALGORITHM ------------- MD = 2 ELEC = 10 -------------------------------- + Density error is +0.000000000431 + + charge density convergence is achieved + final etot is -219.492968914185 eV ><><><><><><><><><><><><><><><><><><><><><>< @@ -490,12 +458,12 @@ Kenetic Term is +0.000000 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 +1.004871 -1.739881 -2.441947 - H2 -3.252618 +0.393216 -0.201464 - H3 +1.449497 +2.920979 -0.074231 - H4 +0.723985 -1.478039 +2.737075 - C1 +0.074265 -0.096275 -0.019433 + atom x y z + H1 +0.49025494 -0.86039958 -1.20570083 + H2 -1.76382370 +0.18895466 -0.09843194 + H3 +0.72520265 +1.42096166 -0.01878483 + H4 +0.37884284 -0.78455333 +1.49561282 + C1 +0.16952328 +0.03503658 -0.17269523 ><><><><><><><><><><><><><><><><><><><><><>< @@ -504,113 +472,178 @@ Kenetic Term is +0.000000 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - +8.239066 +0.040673 +0.022701 - +0.040673 +8.146118 -0.028152 - +0.022701 -0.028152 +8.029180 + +4.553376 -0.021360 +0.084915 + -0.021360 +4.214380 -0.113669 + +0.084915 -0.113669 +4.372736 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 1 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +16.387160 Kbar -Virial Term is +16.276243 Kbar -Kenetic Term is +0.110917 Kbar +Virtual Pressure is +4.468046 Kbar +Virial Term is +4.380164 Kbar +Kenetic Term is +0.087882 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 2 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.108578 (Rydberg) - NVT Temperature : +526.047604 (K) - NVT Kinetic energy : +0.019991 (Rydberg) - NVT Potential energy : -16.128576 (Rydberg) - maxForce : +0.004075 - maxStep : +0.098572 - MD_STEP SystemE Conserved DeltaE Temperature - +2 -8.064288 -8.054289 +0.000000 +1063.334415 + MD STRESS (KBAR) - PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +54.857143 +6.240000 + ><><><><><><><><><><><><><><><><><><><><><>< - Density error is +0.019351753103 + +4.628332 -0.038761 +0.085917 + -0.038761 +4.315308 -0.131320 + +0.085917 -0.131320 +4.460499 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 - PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.340000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 1 -------------------------------- - Density error is +0.000283196908 + Density error is +0.024594159592 - PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.071429 +0.550000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 2 -------------------------------- - Density error is +0.000097414254 + Density error is +0.005534035993 - PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.785714 +0.410000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 3 -------------------------------- - Density error is +0.000008367964 + Density error is +0.003088913442 - PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.857143 +0.540000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 4 -------------------------------- - Density error is +0.000001252601 + Density error is +0.000157548989 - PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.642857 +0.510000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 5 -------------------------------- - Density error is +0.000000066252 + Density error is +0.000009096313 - PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.071429 +0.670000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 6 -------------------------------- - Density error is +0.000000013589 + Density error is +0.000002928976 - PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.571429 +0.610000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 7 -------------------------------- - Density error is +0.000000024404 + Density error is +0.000001094513 - PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.320000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 8 -------------------------------- - Density error is +0.000000010839 + Density error is +0.000000078221 - PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.071429 +0.340000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 9 -------------------------------- - Density error is +0.000000002800 + Density error is +0.000000005822 - PW ALGORITHM --------------- ION=+3 ELEC=+11 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.000000 +0.550000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 10 -------------------------------- - Density error is +0.000000000052 + Density error is +0.000000000775 charge density convergence is achieved - final etot is -219.862433615028 eV + final etot is -219.608412824317 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.16002510 -0.30887491 -0.43098457 + H2 -0.83438114 +0.05437479 -0.02141281 + H3 +0.29374672 +0.52330577 +0.02732362 + H4 +0.14605261 -0.32566633 +0.68804044 + C1 +0.23455671 +0.05686068 -0.26296669 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.098185 +0.007527 +0.104271 + +0.007527 +1.613231 -0.120516 + +0.104271 -0.120516 +1.859916 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 2 + ------------------------------------------- +output Pressure for check! +Virtual Pressure is +2.031062 Kbar +Virial Term is +1.857111 Kbar +Kenetic Term is +0.173952 Kbar + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.265906 -0.014782 +0.112736 + -0.014782 +1.796291 -0.144526 + +0.112736 -0.144526 +2.030990 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 1 -------------------------------- + + Density error is +0.022940518361 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 2 -------------------------------- + + Density error is +0.005222919162 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 3 -------------------------------- + + Density error is +0.002973846634 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 4 -------------------------------- + + Density error is +0.000161676383 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 5 -------------------------------- + + Density error is +0.000006384706 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 6 -------------------------------- + + Density error is +0.000002108229 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 7 -------------------------------- + + Density error is +0.000000600476 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 8 -------------------------------- + + Density error is +0.000000092867 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 9 -------------------------------- + + Density error is +0.000000005281 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 10 -------------------------------- + + Density error is +0.000000000291 + + charge density convergence is achieved + final etot is -219.633913127181 eV + ><><><><><><><><><><><><><><><><><><><><><>< TOTAL-FORCE (eV/Angstrom) ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 +0.308191 -0.535728 -0.757725 - H2 -0.975237 +0.122318 -0.058835 - H3 +0.431328 +0.882198 -0.020974 - H4 +0.218386 -0.449293 +0.842665 - C1 +0.017332 -0.019495 -0.005131 + atom x y z + H1 -0.10149676 +0.12508314 +0.18002539 + H2 +0.00865439 -0.06285089 +0.05043301 + H3 -0.05771566 -0.19843987 +0.06496074 + H4 -0.05642669 +0.07369607 -0.02676084 + C1 +0.20698471 +0.06251155 -0.26865830 ><><><><><><><><><><><><><><><><><><><><><>< @@ -619,33 +652,33 @@ Kenetic Term is +0.110917 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - +2.590889 -0.001256 -0.000685 - -0.001256 +2.591786 +0.001012 - -0.000685 +0.001012 +2.595960 + -0.161231 +0.065000 +0.065454 + +0.065000 -0.596004 -0.045760 + +0.065454 -0.045760 -0.344891 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 3 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +5.870656 Kbar -Virial Term is +5.185757 Kbar -Kenetic Term is +0.684900 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 3 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.111086 (Rydberg) - NVT Temperature : +1266.849197 (K) - NVT Kinetic energy : +0.048143 (Rydberg) - NVT Potential energy : -16.159585 (Rydberg) - maxForce : +0.000367 - maxStep : +0.114449 - MD_STEP SystemE Conserved DeltaE Temperature - +3 -8.079793 -8.055543 +0.000000 +1452.963348 +Virtual Pressure is -0.281288 Kbar +Virial Term is -0.367375 Kbar +Kenetic Term is +0.086088 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.072045 +0.056002 +0.072032 + +0.056002 -0.511726 -0.057839 + +0.072032 -0.057839 -0.260091 -------------------------------------------- - !FINAL_ETOT_IS -219.8624336150282090 eV + !FINAL_ETOT_IS -219.6339131271808753 eV -------------------------------------------- @@ -654,59 +687,84 @@ Kenetic Term is +0.684900 Kbar |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +67.074 15 +4.47 +100.00 % - Run_pw plane_wave_line +67.04 1 +67.04 +99.95 % - PW_Basis gen_pw +0.26 1 +0.26 +0.39 % - Run_MD_PW md_cells_pw +66.70 1 +66.70 +99.45 % - ppcell_vl init_vloc +0.12 1 +0.12 +0.18 % - Potential init_pot +0.46 4 +0.11 +0.68 % - FFT FFT3D +26.79 8433 +0.00 +39.94 % - Charge atomic_rho +0.12 7 +0.02 +0.18 % - Potential v_of_rho +3.52 36 +0.10 +5.25 % - H_XC_pw v_xc +3.31 39 +0.08 +4.93 % - H_Hartree_pw v_hartree +0.42 36 +0.01 +0.63 % - wavefunc wfcinit +1.06 4 +0.26 +1.58 % - pp_cell_vnl getvnl +0.15 42 +0.00 +0.22 % - Hamilt_PW diagH_subspace +3.50 36 +0.10 +5.21 % - Hamilt_PW h_psi +27.80 3259 +0.01 +41.45 % - Hamilt_PW vloc +25.80 3259 +0.01 +38.46 % - Hamilt_PW vnl +1.91 3259 +0.00 +2.85 % - Hamilt_PW add_nonlocal_pp +0.90 3259 +0.00 +1.35 % - Run_MD_PW md_ions_pw +66.15 1 +66.15 +98.63 % - Electrons self_consistent +62.27 3 +20.76 +92.84 % - Electrons c_bands +29.33 32 +0.92 +43.73 % - Hamilt diagH_pw +29.20 32 +0.91 +43.54 % - Diago_CG diag +26.09 34 +0.77 +38.90 % - Charge sum_band +2.94 32 +0.09 +4.38 % - Charge rho_mpi +1.08 32 +0.03 +1.61 % - Charge mix_rho +0.97 32 +0.03 +1.45 % - Forces cal_force_nl +0.24 3 +0.08 +0.36 % - Stress_PW cal_stress +1.94 3 +0.65 +2.89 % - Stress_Func stress_ew +22.20 2 +11.10 +33.10 % - Force_Func stress_ew +22.20 2 +11.10 +33.10 % - Stress_Func stress_gga +0.13 3 +0.04 +0.19 % - Stress_Func stres_nl +1.63 3 +0.54 +2.43 % + total +50.10576 11 +4.56 +100.00% + Run_lcao lcao_line +50.07728 1 +50.08 +99.94% + PW_Basis gen_pw +0.32423 1 +0.32 +0.65% + ORB_control set_orb_tables +1.00186 1 +1.00 +2.00% + ORB_gen_tables gen_tables +1.00186 1 +1.00 +2.00% + ORB_table_phi init_Table +0.62925 1 +0.63 +1.26% + ORB_table_phi cal_ST_Phi12_R +0.62412 126 +0.00 +1.25% + ORB_table_beta init_Table_Beta +0.22784 1 +0.23 +0.45% + ORB_table_beta VNL_PhiBeta_R +0.22637 56 +0.00 +0.45% + Potential init_pot +1.98120 8 +0.25 +3.95% + Potential set_local_pot +0.12809 8 +0.02 +0.26% + FFT FFT3D +8.39921 729 +0.01 +16.76% + Charge atomic_rho +0.18136 7 +0.03 +0.36% + Potential v_of_rho +11.06614 50 +0.22 +22.09% + XC_Functional v_xc +10.17416 54 +0.19 +20.31% + H_Hartree_pw v_hartree +1.55105 50 +0.03 +3.10% + Run_MD_LCAO opt_ions +48.33155 1 +48.33 +96.46% + NVT_NHC setup +13.23980 1 +13.24 +26.42% + MD_func force_stress +25.25482 2 +12.63 +50.40% + LOOP_elec solve_elec_stru +36.73914 4 +9.18 +73.32% + LOOP_elec set_matrix_grid +0.27334 4 +0.07 +0.55% + Grid_Technique init +0.27228 4 +0.07 +0.54% + Grid_BigCellgrid_expansion_index +0.17445 8 +0.02 +0.35% + LOOP_elec solver +36.46298 4 +9.12 +72.77% + ELEC_scf scf +36.46297 4 +9.12 +72.77% + ELEC_cbands_k cal_bands +13.00063 42 +0.31 +25.95% + Gint_k vlocal +5.98284 42 +0.14 +11.94% + Efficience each_k +6.96827 42 +0.17 +13.91% + Efficience H_k +6.91588 42 +0.16 +13.80% + LCAO_Hamilt calculate_Hk +6.91580 42 +0.16 +13.80% + Gint_k folding_vl_k +6.91479 42 +0.16 +13.80% + Gint_k Distri +6.91407 42 +0.16 +13.80% + Local_Orbital_Cha sum_bands +11.29601 42 +0.27 +22.54% + Gint_k cal_rho_k +5.36589 42 +0.13 +10.71% + Charge mix_rho +2.55638 42 +0.06 +5.10% + Force_Stress_LCAO getForceStress +10.60361 4 +2.65 +21.16% + Forces cal_force_loc +0.15708 4 +0.04 +0.31% + Stress_Func stress_loc +0.17575 4 +0.04 +0.35% + Stress_Func stress_har +0.14552 4 +0.04 +0.29% + Stress_Func stress_gga +0.41948 4 +0.10 +0.84% + Force_LCAO_k ftable_k +8.43132 4 +2.11 +16.83% + Force_LCAO_k cal_fvl_dphi_k +8.41336 4 +2.10 +16.79% + Gint_k svl_k_RealSpace +7.44687 4 +1.86 +14.86% + Gint_k evaluate_vl_force +0.94824 133427 +0.00 +1.89% + Gint_k evaluate_vl_stress +1.74281 133427 +0.00 +3.48% + Gint_k folding_force +4.25683 4 +1.06 +8.50% + MD_func md_force_stress +23.39869 2 +11.70 +46.70% ---------------------------------------------------------------------------------------- CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +70.3196 - Charge_Pulay Rrho +13.1836 - Charge_Pulay dRrho +11.5356 - Charge_Pulay drho +11.5356 - Use_FFT porter +3.2959 - PW_Basis struc_fac +2.5457 - wavefunc evc +2.2321 - Charge rho +1.6479 - Charge rho_save +1.6479 - Charge rho_core +1.6479 - Potential vltot +1.6479 - Potential vr +1.6479 - Potential vr_eff +1.6479 - Potential vr_eff1 +1.6479 - Potential vnew +1.6479 - Charge_Pulay rho_save2 +1.6479 + +1164.1075 + ORB_table_phi Jl(x) +131.0928 + Charge_Pulay Rrho +26.3672 + Charge_Pulay dRrho +23.0713 + Charge_Pulay drho +23.0713 + Use_FFT porter +6.5918 + Grid_Meshcell index2normal +5.8017 + Grid_Meshcell index2ucell +5.8017 + PW_Basis struc_fac +5.0912 + ORB_table_phi Table_SR&TR +3.6736 + Charge rho +3.2959 + Charge rho_save +3.2959 + Charge rho_core +3.2959 + Potential vltot +3.2959 + Potential vr +3.2959 + Potential vr_eff +3.2959 + Potential vr_eff1 +3.2959 + Potential vnew +3.2959 + Charge_Pulay rho_save2 +3.2959 + init_meshball meshball_pos +2.1575 + Charge rhog +1.2728 + Charge rhog_save +1.2728 + Charge kin_r +1.2728 + Charge kin_r_save +1.2728 + Charge rhog_core +1.2728 + ORB_table_beta Table_NR +1.1560 ---------------------------------------------------------- - Start Time : Fri Nov 12 18:15:13 2021 - Finish Time : Fri Nov 12 18:16:20 2021 - Total Time : 0 h 1 mins 7 secs + Start Time : Sun Apr 17 15:10:23 2022 + Finish Time : Sun Apr 17 15:11:13 2022 + Total Time : 0 h 0 mins 50 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU index 9df80429c..4bf80593d 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU @@ -15,11 +15,18 @@ Cartesian # Cartesian(Unit is LATTICE_CONSTANT) H 0.0 4 -5.097444375976 3.891293394194 3.462261233691 1 1 1 -3.796292512908 4.557084804487 4.168353214339 1 1 1 -5.223523410907 5.328269903334 4.206766613435 1 1 1 -5.007077103527 3.977914209143 5.081170168915 1 1 1 +5.113541511412 3.863321620159 3.422849404241 1 1 1 +3.744792402058 4.563437069250 4.165241539141 1 1 1 +5.246389147225 5.374789014111 4.205651315346 1 1 1 +5.018535899770 3.954367806503 5.125120082345 1 1 1 C 0.0 1 -4.779784174238 4.440311459394 4.230030312730 1 1 1 +4.780862617100 4.438958260529 4.229719202017 1 1 1 + +NUMERICAL_ORBITAL +H_gga_8au_60Ry_2s1p.orb +C_gga_8au_60Ry_2s2p1d.orb + +NUMERICAL_DESCRIPTOR +jle.orb diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT index c3181c397..f38b2d7d0 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT @@ -1,20 +1,17 @@ INPUT_PARAMETERS calculation md -atom_file STRU -kpoint_file KPT pseudo_dir ./ ntype 2 symmetry 1 ecutwfc 90 -npool 1 - mixing_type pulay mixing_beta 0.4 +basis_type lcao +md_nstep 3 +cal_stress 1 +deepks_model model.ptg -nstep 3 -force_thr_ev 0.02 -#move_method cg -out_stru 0 -stress 1 +md_tfirst 10 +md_tfreq 0.1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT deleted file mode 100644 index 63bd0ed40..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT +++ /dev/null @@ -1,263 +0,0 @@ -INPUT_PARAMETERS -#Parameters (1.General) -suffix ABACUS #the name of main output directory -latname test #the name of lattice name -atom_file STRU #the filename of file containing atom positions -kpoint_file KPT #the name of file containing k points -pseudo_dir .// #the directory containing pseudo files -orbital_dir #the directory containing orbital files -pseudo_type auto #the type pseudo files -pseudo_rcut 15 #cut-off radius for radial integration -renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE -lmaxmax 2 #maximum of l channels used -dft_functional none #exchange correlation functional -calculation md #test; scf; relax; nscf; ienvelope; istate; -ntype 2 #atom species number -nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin -nbands 0 #number of bands -nbands_sto 0 #number of stochastic bands -nbands_istate 5 #number of bands around Fermi level for istate calulation -nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT -symmetry 0 #turn symmetry on or off -set_vel 0 #read velocity from STRU or not -symmetry_prec 1e-05 #accuracy for symmetry -nelec 0 #input number of electrons -tot_magnetization 0 #total magnetization of the system - -#Parameters (2.PW) -ecutwfc 90 ##energy cutoff for wave functions -diago_cg_maxiter 50 #max iteration number for cg -diago_cg_prec 1 #diago_cg_prec -ethr 0.01 #threshold for eigenvalues is cg electron iterations -dr2 1e-09 #charge density error -start_wfc atomic #start wave functions are from 'atomic' or 'file' -start_charge atomic #start charge is from 'atomic' or file -charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA -out_charge 0 #>0 output charge density for selected electron steps -out_potential 0 #output realspace potential -out_wf 0 #output wave functions -out_dos 0 #output energy and dos -out_band 0 #output energy and band structure -restart_save 0 #print to disk every step for restart -restart_load 0 #restart from disk -read_file_dir auto #directory of files for reading -nx 0 #number of points along x axis for FFT grid -ny 0 #number of points along y axis for FFT grid -nz 0 #number of points along z axis for FFT grid -cell_factor 1.2 #used in the construction of the pseudopotential tables - -#Parameters (3.Relaxation) -ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx -niter 40 ##number of electron iterations -force_set 0 #output the force_set or not -nstep 3 #number of ion iteration steps -out_stru 0 #output the structure files after each ion step -force_thr 0.00077787 #force threshold, unit: Ry/Bohr -force_thr_ev 0.02 #force threshold, unit: eV/Angstrom -force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom -cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom -stress_thr 0.01 #stress threshold -press1 0 #target pressure, unit: KBar -press2 0 #target pressure, unit: KBar -press3 0 #target pressure, unit: KBar -bfgs_w1 0.01 #wolfe condition 1 for bfgs -bfgs_w2 0.5 #wolfe condition 2 for bfgs -trust_radius_max 0.8 #maximal trust radius, unit: Bohr -trust_radius_min 1e-05 #minimal trust radius, unit: Bohr -trust_radius_ini 0.5 #initial trust radius, unit: Bohr -stress 1 #calculate the stress or not -fixed_axes None #which axes are fixed -move_method cg #bfgs; sd; cg; cg_bfgs; -out_level m #ie(for electrons); i(for ions); -out_dm 0 #>0 output density matrix -out_descriptor 0 #>0 compute descriptor for deepks -lmax_descriptor 2 #>0 lmax used in descriptor for deepks - -#Parameters (4.LCAO) -basis_type pw #PW; LCAO in pw; LCAO -new_dm 1 #Type of density matrix; 0: old 1: new -search_radius -1 #input search radius (Bohr) -search_pbc 1 #input periodic boundary condition -lcao_ecut 0 #energy cutoff for LCAO -lcao_dk 0.01 #delta k for 1D integration in LCAO -lcao_dr 0.01 #delta r for 1D integration in LCAO -lcao_rmax 30 #max R for 1D two-center integration table -out_hs 0 #output H and S matrix -out_hs2 0 #output H(R) and S(R) matrix -out_r 0 #output r(R) matrix -out_lowf 0 #ouput LCAO wave functions -bx 1 #division of an element grid in FFT grid along x -by 1 #division of an element grid in FFT grid along y -bz 1 #division of an element grid in FFT grid along z - -#Parameters (5.Smearing) -smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv -sigma 0.01 #energy range for smearing - -#Parameters (6.Charge Mixing) -mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden -mixing_beta 0.4 #mixing parameter: 0 means no new charge -mixing_ndim 8 #mixing dimension in pulay -mixing_gg0 0 #mixing parameter in kerker - -#Parameters (7.DOS) -dos_emin_ev -15 #minimal range for dos -dos_emax_ev 15 #maximal range for dos -dos_edelta_ev 0.01 #delta energy for dos -dos_scale 0.01 #scale dos range by -dos_sigma 0.07 #gauss b coefficeinet(default=0.07) - -#Parameters (8.Technique) -gamma_only 0 #gamma only, only used in LCAO basis -diago_proc 8 #number of proc used to diago -npool 1 #number of pools for k points, pw only -mem_saver 0 #memory saver for many k points used -printe 100 #print band energy for selectively ionic steps - -#Parameters (9.SIAO) -selinv_npole 40 #number of selected poles -selinv_temp 2000 #temperature for Fermi-Dirac distribution -selinv_gap 0 #supposed gap in the calculation -selinv_deltae 2 #expected energy range -selinv_mu -1 #chosen mu as Fermi energy -selinv_threshold 0.001 #threshold for calculated electron number -selinv_niter 50 #max number of steps to update mu - -#Parameters (10.Molecular dynamics) -md_mdtype 1 #choose ensemble -md_potential FP #choose potential -md_dt 1 #time step -mnhc 4 #number of Nose-Hoover chains -md_qmass 1 #mass of thermostat -md_tfirst 0 #temperature first -md_tlast 0 #temperature last -md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD -md_mdoutpath mdoutput #output path of md -md_rstmd 0 #whether restart -md_fixtemperature 1 #period to change temperature -md_ediff 0.0001 #parameter for constraining total energy change -md_ediffg 0.001 #parameter for constraining max force change -NVT_tau 0 #parameter for adjust effect of thermostat -NVT_control 1 #choose which thermostat used in NVT ensemble -rcut_lj 8.5 #cutoff radius of LJ potential -epsilon_lj 0.01032 #the value of epsilon for LJ potential -sigma_lj 3.405 #the value of sigma for LJ potential - -#Parameters (11.Efield) -efield 0 #add electric field -edir 1 #add electric field -emaxpos 0.5 #maximal position of efield [0,1) -eopreg 0.1 #where sawlike potential decrease -eamp 0.001 #amplitute of the efield, unit is a.u. -eamp_v 0.05144 #amplitute of the efield, unit is V/A - -#Parameters (12.Test) -out_alllog 0 #output information for each processor, when parallel -nurse 0 #for coders -colour 0 #for coders, make their live colourful -t_in_h 1 #calculate the kinetic energy or not -vl_in_h 1 #calculate the local potential or not -vnl_in_h 1 #calculate the nonlocal potential or not -vh_in_h 1 #calculate the hartree potential or not -vxc_in_h 1 #calculate the xc potential or not -vion_in_h 1 #calculate the local ionic potential or not -test_force 0 #test the force -test_stress 0 #test the force - -#Parameters (13.Other Methods) -mlwf_flag 0 #turn MLWF on or off -opt_epsilon2 0 #calculate the dielectic function -opt_nbands 0 #number of bands for optical calculation - -#Parameters (14.VdW Correction) -vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj -vdw_s6 default #scale parameter of d2/d3_0/d3_bj -vdw_s8 default #scale parameter of d3_0/d3_bj -vdw_a1 default #damping parameter of d3_0/d3_bj -vdw_a2 default #damping parameter of d3_bj -vdw_d 20 #damping parameter of d2 -vdw_abc 0 #third-order term? -vdw_C6_file default #filename of C6 -vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 -vdw_R0_file default #filename of R0 -vdw_R0_unit A #unit of R0, A or Bohr -vdw_model radius #expression model of periodic structure, radius or period -vdw_radius default #radius cutoff for periodic structure -vdw_radius_unit Bohr #unit of radius cutoff for periodic structure -vdw_cn_thr 40 #radius cutoff for cn -vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom -vdw_period 3 3 3 #periods of periodic structure - -#Parameters (15.spectrum) -spectral_type None #the type of the calculated spectrum -spectral_method 0 #0: tddft(linear response) -kernel_type rpa #the kernel type: rpa, tdlda ... -eels_method 0 #0: hilbert_transform method; 1: standard method -absorption_method 0 #0: vasp's method 1: pwscf's method -system bulk #the calculate system -eta 0.05 #eta(Ry) -domega 0.01 #domega(Ry) -nomega 300 #nomega -ecut_chi 1 #the dimension of chi matrix -q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate -q_direction 1 0 0 #the q direction -nq 1 #the total number of qpoints for calculation -out_epsilon 1 #output epsilon or not -out_chi 0 #output chi or not -out_chi0 0 #output chi0 or not -fermi_level 0 #the change of the fermi_level(Ry) -coulomb_cutoff 0 # turn on the coulomb_cutoff or not -kmesh_interpolation 0 #calculting -qcar 0 0 0 #(unit: 2PI/lat0) -ocp 0 #change occupation or not -ocp_set none #set occupation -lcao_box 10 10 10 #the scale for searching the existence of the overlap - mulliken 0 # mulliken charge or not -intrasmear 0 #Eta -shift 0 #shift -metalcalc 0 #metal or not -eps_degauss 0.01 #degauss in calculating epsilon0 -noncolin 0 #using non-collinear-spin -lspinorb 0 #consider the spin-orbit interaction - -#Parameters (17.exx) -exx_hybrid_type no #no, hf, pbe0, hse or opt_orb -exx_hybrid_alpha 0.25 # -exx_hse_omega 0.11 # -exx_separate_loop 1 #0 or 1 -exx_hybrid_step 100 # -exx_lambda 0.3 # -exx_pca_threshold 0 # -exx_c_threshold 0 # -exx_v_threshold 0 # -exx_dm_threshold 0 # -exx_schwarz_threshold0 # -exx_cauchy_threshold0 # -exx_ccp_threshold 1e-08 # -exx_ccp_rmesh_times 10 # -exx_distribute_type htime #htime or kmeans1 or kmeans2 -exx_opt_orb_lmax 0 # -exx_opt_orb_ecut 0 # -exx_opt_orb_tolerence0 # - -#Parameters (17.tddft) -tddft 0 #calculate tddft or not -td_dr2 1e-09 #threshold for electronic iteration of tddft -td_dt 0.02 #time of ion step -td_force_dt 0.02 #time of force change -td_val_elec_01 1 #td_val_elec_01 -td_val_elec_02 1 #td_val_elec_02 -td_val_elec_03 1 #td_val_elec_03 -td_vext 0 #add extern potential or not -td_vext_dire 1 #extern potential direction -td_timescale 0.5 #extern potential td_timescale -td_vexttype 1 #extern potential type -td_vextout 0 #output extern potential or not -td_dipoleout 0 #output dipole or not - -#Parameters (18.berry_wannier) -berry_phase 0 #calculate berry phase or not -gdir 3 #calculate the polarization in the direction of the lattice std::vector -towannier90 0 #use wannier90 code interface or not -nnkpfile seedname.nnkp #the wannier90 code nnkp file name -wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/MD_dump b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/MD_dump new file mode 100644 index 000000000..69ea8143c --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/MD_dump @@ -0,0 +1,72 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.679120503366 0.000000000000 0.000000000000 + 0.064831950309 9.384493544041 0.000000000000 + 0.210894191441 -0.031988736496 9.460865078677 +VIRIAL (KBAR) + 5.640169039135 0.118557619965 0.100345423315 + 0.118557619965 5.482515827407 -0.147097161241 + 0.100345423315 -0.147097161241 5.095791410360 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.113130840122 3.868695648576 3.415487569497 0.600673184035 -1.059740442673 -1.418495993188 + 1 H 3.744651237763 4.563580660532 4.164111061024 -2.191135947068 0.245188540314 -0.119090216567 + 2 H 5.240406959488 5.372954887162 4.205693454922 0.970609293432 1.961304510034 -0.029986389419 + 3 H 5.018637879218 3.954691355167 5.129125905570 0.469126098480 -0.976170970669 1.745238499110 + 4 C 4.777789211889 4.437703391265 4.232924722816 0.150727371121 -0.170581637006 -0.177665899936 + + +MDSTEP: 1 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.679120503366 0.000000000000 0.000000000000 + 0.064831950309 9.384493544041 0.000000000000 + 0.210894191441 -0.031988736496 9.460865078677 +VIRIAL (KBAR) + 4.678551039909 0.065179656533 0.157649293879 + 0.065179656533 4.238967373425 -0.212375925046 + 0.157649293879 -0.212375925046 4.076335855843 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.119291530616 3.862413938554 3.408309247541 0.442095295825 -0.801587535162 -1.052519150428 + 1 H 3.737114387708 4.567707590805 4.158438789249 -1.844676097365 0.181666395548 -0.085358985581 + 2 H 5.244273865813 5.384140784850 4.201093321848 0.750707433879 1.480714365731 0.000930221355 + 3 H 5.021865320527 3.949477758617 5.135847806351 0.371343245256 -0.790918808758 1.452768625603 + 4 C 4.777309284031 4.437382986473 4.233825193810 0.280530122406 -0.069874417359 -0.315820710948 + + +MDSTEP: 2 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.679120503366 0.000000000000 0.000000000000 + 0.064831950309 9.384493544041 0.000000000000 + 0.210894191441 -0.031988736496 9.460865078677 +VIRIAL (KBAR) + 2.122225562381 0.032179859022 0.116764119158 + 0.032179859022 1.657347414425 -0.126403059763 + 0.116764119158 -0.126403059763 1.723459869010 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.129194979428 3.849057221794 3.391777932413 0.148698675982 -0.317989928108 -0.370018432200 + 1 H 3.712887215270 4.573278250279 4.152308702254 -0.854502702867 0.041198009333 -0.002061590459 + 2 H 5.254885802976 5.408420513347 4.196773592900 0.299717378039 0.540324762250 0.049085353741 + 3 H 5.028351577920 3.937225158159 5.155667664729 0.139991173922 -0.338641889018 0.665750409303 + 4 C 4.777076422524 4.437027033157 4.234426239844 0.266095474923 0.075109045543 -0.342755740386 + + +MDSTEP: 3 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 9.679120503366 0.000000000000 0.000000000000 + 0.064831950309 9.384493544041 0.000000000000 + 0.210894191441 -0.031988736496 9.460865078677 +VIRIAL (KBAR) + -0.221393607103 0.045650693865 0.032718214304 + 0.045650693865 -0.552324429324 0.014848809564 + 0.032718214304 0.014848809564 -0.370470671582 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 5.137770370778 3.836513194293 3.376448676476 -0.089449994948 0.074427957375 0.180006734252 + 1 H 3.687820381885 4.577748257190 4.147750331999 0.033387754857 -0.079840940835 0.073540843258 + 2 H 5.265244249465 5.430908724294 4.193982471445 -0.066296870019 -0.214350389585 0.086916875019 + 3 H 5.034322953422 3.925327003983 5.175896961997 -0.062788628675 0.059757319489 -0.037683225140 + 4 C 4.777089987303 4.436815862094 4.234631822357 0.185147738786 0.160006053556 -0.302781227389 + + diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD deleted file mode 100644 index 10302ea51..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD +++ /dev/null @@ -1,27 +0,0 @@ -ATOMIC_SPECIES -H 1.008 H_ONCV_PBE-1.0.upf -C 12.01 C_ONCV_PBE-1.0.upf - -LATTICE_CONSTANT -1.88972612546 - -LATTICE_VECTORS -9.70691437102 0 0 #latvec1 --0.281382603073 9.68406871255 0 #latvec2 -0.158246266482 -0.163817668352 9.58297385826 #latvec3 - -ATOMIC_POSITIONS -Direct - -H #label -0 #magnetism -4 #number of atoms -0.535461381214 0.40022105074 0.350517908729 1 1 1 0 0 0 -0.384059480088 0.479432956913 0.433779873798 1 1 1 0 0 0 -0.553450272577 0.569838705306 0.439037455701 1 1 1 0 0 0 -0.521761060531 0.414199303256 0.541959017837 1 1 1 0 0 0 - -C #label -0 #magnetism -1 #number of atoms -0.498801629025 0.465841043252 0.44124373684 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif deleted file mode 100644 index 233b8c367..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.70691 -_cell_length_b 9.68815 -_cell_length_c 9.58568 -_cell_angle_alpha 91.0063 -_cell_angle_beta 89.0541 -_cell_angle_gamma 91.6643 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.53097 0.408053 0.361246 -H 0.398147 0.47768 0.434684 -H 0.54717 0.557856 0.43944 -H 0.51918 0.420134 0.530801 -C 0.498731 0.465842 0.441171 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif deleted file mode 100644 index 5a5b6ed05..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.70691 -_cell_length_b 9.68815 -_cell_length_c 9.58568 -_cell_angle_alpha 91.0063 -_cell_angle_beta 89.0541 -_cell_angle_gamma 91.6643 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.531666 0.406832 0.359568 -H 0.395926 0.477951 0.434543 -H 0.548145 0.559719 0.439384 -H 0.519578 0.419226 0.532529 -C 0.498744 0.465842 0.441183 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif deleted file mode 100644 index 898144995..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.70691 -_cell_length_b 9.68815 -_cell_length_c 9.58568 -_cell_angle_alpha 91.0063 -_cell_angle_beta 89.0541 -_cell_angle_gamma 91.6643 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.533403 0.403793 0.355398 -H 0.390433 0.478629 0.434192 -H 0.550578 0.564369 0.439236 -H 0.520575 0.416939 0.536854 -C 0.498773 0.465841 0.441212 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif deleted file mode 100644 index a10888c1f..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.70691 -_cell_length_b 9.68815 -_cell_length_c 9.58568 -_cell_angle_alpha 91.0063 -_cell_angle_beta 89.0541 -_cell_angle_gamma 91.6643 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.535461 0.400221 0.350518 -H 0.384059 0.479433 0.43378 -H 0.55345 0.569839 0.439037 -H 0.521761 0.414199 0.541959 -C 0.498802 0.465841 0.441244 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log index e60ae9ad2..48b0535ae 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log @@ -6,8 +6,8 @@ Website: http://abacus.ustc.edu.cn/ Version: Parallel, in development - Processor Number is 8 - Start Time is Fri Nov 12 18:16:22 2021 + Processor Number is 4 + Start Time is Sun Apr 17 15:11:14 2022 ------------------------------------------------------------------------------------ @@ -18,7 +18,7 @@ orbital_dir = pseudo_type = auto DRANK = 1 - DSIZE = 8 + DSIZE = 4 DCOLOR = 1 GRANK = 1 GSIZE = 1 @@ -52,9 +52,8 @@ READING ATOM TYPE 1 atom label = H - L=0, number of zeta = 1 + L=0, number of zeta = 2 L=1, number of zeta = 1 - L=2, number of zeta = 1 number of atom for this type = 4 start magnetization = FALSE start magnetization = FALSE @@ -63,8 +62,8 @@ READING ATOM TYPE 2 atom label = C - L=0, number of zeta = 1 - L=1, number of zeta = 1 + L=0, number of zeta = 2 + L=1, number of zeta = 2 L=2, number of zeta = 1 number of atom for this type = 1 start magnetization = FALSE @@ -73,24 +72,28 @@ CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). atom x y z mag vx vy vz - tauc_H1 5.09642839721 3.89243558658 3.46181024571 0 0 0 0 - tauc_H2 3.79915812176 4.55467455263 4.16556354192 0 0 0 0 - tauc_H3 5.22389947082 5.33033053366 4.21113724544 0 0 0 0 - tauc_H4 5.00541687456 3.98165554454 5.08665008197 0 0 0 0 - tauc_C1 4.77987185192 4.43897624107 4.22772783445 0 0 0 0 + tauc_H1 5.11313084012 3.86869564858 3.4154875695 0 0 0 0 + tauc_H2 3.74465123776 4.56358066053 4.16411106102 0 0 0 0 + tauc_H3 5.24040695949 5.37295488716 4.20569345492 0 0 0 0 + tauc_H4 5.01863787922 3.95469135517 5.12912590557 0 0 0 0 + tauc_C1 4.77778921189 4.43770339127 4.23292472282 0 0 0 0 + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: H_gga_8au_60Ry_2s1p.orb + orbital file: C_gga_8au_60Ry_2s2p1d.orb - Volume (Bohr^3) = 6079.05350607 - Volume (A^3) = 900.821712756 + Volume (Bohr^3) = 5799.28146373 + Volume (A^3) = 859.363822953 Lattice vectors: (Cartesian coordinate: in unit of a_0) - +9.70691437102 +0 +0 - -0.281382603073 +9.68406871255 +0 - +0.158246266482 -0.163817668352 +9.58297385826 + +9.67912050337 +0 +0 + +0.0648319503089 +9.38449354404 +0 + +0.210894191441 -0.0319887364963 +9.46086507868 Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) - +0.103019349072 +0.00299335470133 -0.00165001629058 - -0 +0.10326238172 +0.0017652351819 - +0 -0 +0.104351740367 + +0.10331517204 -0.000713743801774 -0.0023054341492 + -0 +0.106558760503 +0.000360292645836 + +0 -0 +0.105698579536 @@ -117,10 +120,7 @@ Read in pseudopotential file is H_ONCV_PBE-1.0.upf pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = + exchange-correlation functional = PBE nonlocal core correction = 0 valence electrons = 1 lmax = 0 @@ -132,10 +132,7 @@ Read in pseudopotential file is C_ONCV_PBE-1.0.upf pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = + exchange-correlation functional = PBE nonlocal core correction = 0 valence electrons = 4 lmax = 1 @@ -146,7 +143,7 @@ L of projector = 1 L of projector = 1 initial pseudo atomic orbital number = 0 - NLOCAL = 45 + NLOCAL = 33 SETUP THE ELECTRONS NUMBER electron number of element H = 1 @@ -154,8 +151,10 @@ electron number of element C = 4 total electron number of element C = 4 occupied bands = 4 + NLOCAL = 33 NBANDS = 14 - DONE : SETUP UNITCELL Time : 0.070024178247 (SEC) + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.0380957610905 (SEC) @@ -190,7 +189,7 @@ KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT 1 0 0 0 2 - DONE : INIT K-POINTS Time : 0.0716588154319 (SEC) + DONE : INIT K-POINTS Time : 0.0397647852078 (SEC) @@ -213,167 +212,159 @@ SETUP THE PLANE WAVE BASIS energy cutoff for wavefunc (unit:Ry) = 90 - [fft grid for wave functions] = 120, 120, 120 - [fft grid for charge/potential] = 120, 120, 120 - [fft grid division] = 1, 1, 1 - [big fft grid for charge/potential] = 120, 120, 120 - nbxx = 216000 - nrxx = 216000 + [fft grid for wave functions] = 120, 108, 120 + [fft grid for charge/potential] = 120, 108, 120 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 60, 54, 60 + nbxx = 48600 + nrxx = 388800 SETUP PLANE WAVES FOR CHARGE/POTENTIAL - number of plane waves = 701419 - number of sticks = 9633 + number of plane waves = 668909 + number of sticks = 9299 SETUP PLANE WAVES FOR WAVE FUNCTIONS - number of plane waves = 87687 - number of sticks = 2409 + number of plane waves = 83591 + number of sticks = 2323 PARALLEL PW FOR CHARGE/POTENTIAL PROC COLUMNS(POT) PW - 1 1204 87678 - 2 1204 87678 - 3 1205 87677 - 4 1204 87678 - 5 1204 87677 - 6 1204 87677 - 7 1204 87677 - 8 1204 87677 + 1 2325 167228 + 2 2324 167226 + 3 2325 167228 + 4 2325 167227 --------------- sum ------------------- - 8 9633 701419 + 4 9299 668909 PARALLEL PW FOR WAVE FUNCTIONS PROC COLUMNS(W) PW - 1 300 10959 - 2 301 10962 - 3 303 10960 - 4 302 10960 - 5 303 10961 - 6 300 10961 - 7 301 10964 - 8 299 10960 + 1 585 20895 + 2 580 20900 + 3 576 20894 + 4 582 20902 --------------- sum ------------------- - 8 2409 87687 + 4 2323 83591 SETUP COORDINATES OF PLANE WAVES - number of total plane waves = 701419 + number of total plane waves = 668909 SETUP COORDINATES OF PLANE WAVES - number of |g| = 84378 - max |g| = 32.563923009 - min |g| = 0 - DONE : INIT PLANEWAVE Time : 0.350538940344 (SEC) + number of |g| = 159414 + max |g| = 32.5640532433 + min |g| = 0.0106798492305 + DONE : INIT PLANEWAVE Time : 0.489081679843 (SEC) - npwx = 10959 + DONE : INIT CHARGE Time : 0.770516367629 (SEC) - SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS - H non-local projectors: - projector 1 L=0 - projector 2 L=0 - C non-local projectors: - projector 1 L=0 - projector 2 L=0 - projector 3 L=1 - projector 4 L=1 - TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 - DONE : LOCAL POTENTIAL Time : 4.32109053986 (SEC) + DONE : INIT POTENTIAL Time : 0.77587737795 (SEC) - Init Non-Local PseudoPotential table : - Init Non-Local-Pseudopotential done. - DONE : NON-LOCAL POTENTIAL Time : 4.32724457909 (SEC) - start_pot = atomic - DONE : INIT POTENTIAL Time : 4.80582 (SEC) - Make real space PAO into reciprocal space. - max mesh points in Pseudopotential = 601 - dq(describe PAO in reciprocal space) = 0.01 - max q = 1143 + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - number of pseudo atomic orbitals for H is 0 - number of pseudo atomic orbitals for C is 0 - DONE : INIT BASIS Time : 5.09354 (SEC) - ...............Nose-Hoover Chain parameter initialization............... - Temperature = 0 - Temperature2 = 0 - NHC frequency = 0.00120944 - NHC chain = 4 - Qmass = 1822.89 - ............................................................... - PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - K-point CG iter num Time(Sec) - 1 9.785714 1.390000 - Density error is 0.942995755677 + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 953 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + 4 1 1 801 0.01 8 1 1 + 5 2 0 801 0.01 8 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 - PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - K-point CG iter num Time(Sec) - 1 2.285714 0.410000 + SETUP THE TWO-CENTER INTEGRATION TABLES - Density error is 0.099685883319 + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 33 + trace_loc_col dimension = 33 + nloc = 289 + init_chg = atomic + nloc = 289 + searching radius is (Bohr)) = 18.89 + searching radius unit is (Bohr)) = 1.88973 - PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - K-point CG iter num Time(Sec) - 1 4.142857 0.650000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 1 -------------------------------- - Density error is 0.029031982042 + Density error is 0.368881208486 - PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - K-point CG iter num Time(Sec) - 1 4.285714 0.660000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 2 -------------------------------- - Density error is 0.216126036110 + Density error is 0.143521022261 - PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - K-point CG iter num Time(Sec) - 1 3.357143 0.540000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 3 -------------------------------- - Density error is 0.000141170928 + Density error is 0.0734754129089 - PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - K-point CG iter num Time(Sec) - 1 7.357143 1.070000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 4 -------------------------------- - Density error is 0.000036712166 + Density error is 0.00483041498782 - PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - K-point CG iter num Time(Sec) - 1 3.928571 0.680000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 5 -------------------------------- - Density error is 0.000012403136 + Density error is 0.00173364587612 - PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - K-point CG iter num Time(Sec) - 1 4.642857 0.780000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 6 -------------------------------- - Density error is 0.000000169540 + Density error is 0.000105338925335 - PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- - K-point CG iter num Time(Sec) - 1 6.785714 1.080000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 7 -------------------------------- - Density error is 0.000000193385 + Density error is 6.47868339214e-05 - PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- - K-point CG iter num Time(Sec) - 1 4.000000 0.630000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 8 -------------------------------- - Density error is 0.000000002471 + Density error is 1.29512900158e-05 - PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- - K-point CG iter num Time(Sec) - 1 9.000000 1.160000 + LCAO ALGORITHM ------------- MD = 1 ELEC = 9 -------------------------------- - Density error is 0.000000000287 + Density error is 2.29689343972e-06 - charge density convergence is achieved - final etot is -219.132652714524 eV + LCAO ALGORITHM ------------- MD = 1 ELEC = 10 -------------------------------- + + Density error is 2.5633279263e-07 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 11 -------------------------------- + Density error is 1.43568218115e-08 + LCAO ALGORITHM ------------- MD = 1 ELEC = 12 -------------------------------- + + Density error is 1.35671237418e-09 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 13 -------------------------------- + + Density error is 6.32645823916e-10 + + charge density convergence is achieved + final etot is -219.420217336 eV ><><><><><><><><><><><><><><><><><><><><><>< @@ -382,11 +373,11 @@ ><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 +1.427623 -2.413519 -3.360832 - H2 -4.528626 +0.554349 -0.282580 - H3 +1.865702 +3.772834 -0.111599 - H4 +0.916683 -1.897685 +3.461780 - C1 +0.318617 -0.015979 +0.293231 + H1 +0.60067315 -1.0597404 -1.4184959 + H2 -2.1911358 +0.24518852 -0.11909021 + H3 +0.97060923 +1.9613044 -0.029986387 + H4 +0.46912607 -0.97617091 +1.7452384 + C1 +0.15072736 -0.17058163 -0.17766589 ><><><><><><><><><><><><><><><><><><><><><>< @@ -395,88 +386,75 @@ ><><><><><><><><><><><><><><><><><><><><><>< - +10.529622 -0.107421 -0.098680 - -0.107421 +9.970420 +0.216130 - -0.098680 +0.216130 +9.886865 + +5.640169 +0.118558 +0.100345 + +0.118558 +5.482516 -0.147097 + +0.100345 -0.147097 +5.095791 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +20.257937 Kbar -Virial Term is +20.257937 Kbar -Kenetic Term is +0.000000 Kbar +Virtual Pressure is +5.412585 Kbar +Virial Term is +5.406159 Kbar +Kenetic Term is +0.006426 Kbar - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 1 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.105947 (Rydberg) - NVT Temperature : +0.000000 (K) - NVT Kinetic energy : +0.000000 (Rydberg) - NVT Potential energy : -16.105947 (Rydberg) - maxForce : +0.007902 - maxStep : +0.041308 - MD_STEP SystemE Conserved DeltaE Temperature - +1 -8.052974 -8.052974 +0.000000 +171.583724 - PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +54.428571 +6.400000 + ><><><><><><><><><><><><><><><><><><><><><>< - Density error is +0.003416963341 + MD STRESS (KBAR) - PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.340000 + ><><><><><><><><><><><><><><><><><><><><><>< - Density error is +0.000062315805 + +5.644951 +0.119420 +0.096309 + +0.119420 +5.485335 -0.151898 + +0.096309 -0.151898 +5.107470 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 - PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.071429 +0.560000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 1 -------------------------------- - Density error is +0.000015787808 + Density error is +0.010170039282 - PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.357143 +0.480000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 2 -------------------------------- - Density error is +0.000001288949 + Density error is +0.002452018621 - PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.500000 +0.750000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 3 -------------------------------- - Density error is +0.000000182921 + Density error is +0.001326077736 - PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.857143 +0.420000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 4 -------------------------------- - Density error is +0.000000016603 + Density error is +0.000080877382 - PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.285714 +0.700000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 5 -------------------------------- - Density error is +0.000000011064 + Density error is +0.000010764553 - PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.330000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 6 -------------------------------- - Density error is +0.000000004133 + Density error is +0.000001312821 - PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.214286 +0.470000 + LCAO ALGORITHM ------------- MD = 2 ELEC = 7 -------------------------------- - Density error is +0.000000000094 + Density error is +0.000000439436 - charge density convergence is achieved - final etot is -219.442104652403 eV + LCAO ALGORITHM ------------- MD = 2 ELEC = 8 -------------------------------- + + Density error is +0.000000075403 + + LCAO ALGORITHM ------------- MD = 2 ELEC = 9 -------------------------------- + Density error is +0.000000005627 + LCAO ALGORITHM ------------- MD = 2 ELEC = 10 -------------------------------- + + Density error is +0.000000000349 + + charge density convergence is achieved + final etot is -219.493805558154 eV ><><><><><><><><><><><><><><><><><><><><><>< @@ -484,12 +462,12 @@ Kenetic Term is +0.000000 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 +1.068960 -1.799542 -2.503128 - H2 -3.353024 +0.414117 -0.209592 - H3 +1.397261 +2.832427 -0.092488 - H4 +0.691597 -1.440532 +2.608917 - C1 +0.195206 -0.006470 +0.196291 + atom x y z + H1 +0.44209527 -0.80158748 -1.05251908 + H2 -1.84467598 +0.18166638 -0.08535898 + H3 +0.75070739 +1.48071427 +0.00093022 + H4 +0.37134322 -0.79091876 +1.45276853 + C1 +0.28053010 -0.06987441 -0.31582069 ><><><><><><><><><><><><><><><><><><><><><>< @@ -498,94 +476,165 @@ Kenetic Term is +0.000000 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - +7.986919 -0.080516 -0.073538 - -0.080516 +7.635404 +0.126752 - -0.073538 +0.126752 +7.556286 + +4.678551 +0.065180 +0.157649 + +0.065180 +4.238967 -0.212376 + +0.157649 -0.212376 +4.076336 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 1 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +15.557594 Kbar -Virial Term is +15.452406 Kbar -Kenetic Term is +0.105188 Kbar +Virtual Pressure is +4.417092 Kbar +Virial Term is +4.331285 Kbar +Kenetic Term is +0.085807 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 2 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.108768 (Rydberg) - NVT Temperature : +524.091079 (K) - NVT Kinetic energy : +0.019916 (Rydberg) - NVT Potential energy : -16.128691 (Rydberg) - maxForce : +0.004333 - maxStep : +0.101848 - MD_STEP SystemE Conserved DeltaE Temperature - +2 -8.064346 -8.054384 +0.000000 +1059.261288 + +4.757573 +0.051454 +0.163158 + +0.051454 +4.341588 -0.234466 + +0.163158 -0.234466 +4.152114 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 - PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +56.071429 +6.530000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 1 -------------------------------- - Density error is +0.019256453110 + Density error is +0.024396996904 - PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.340000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 2 -------------------------------- - Density error is +0.000283272912 + Density error is +0.005495181923 - PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.214286 +0.570000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 3 -------------------------------- - Density error is +0.000097131520 + Density error is +0.003065556726 - PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.714286 +0.400000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 4 -------------------------------- - Density error is +0.000008019387 + Density error is +0.000166491682 - PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.642857 +0.630000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 5 -------------------------------- - Density error is +0.000001180377 + Density error is +0.000014950420 - PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.571429 +0.500000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 6 -------------------------------- - Density error is +0.000000049998 + Density error is +0.000003046118 - PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.500000 +0.740000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 7 -------------------------------- - Density error is +0.000000005236 + Density error is +0.000001175800 - PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.285714 +0.690000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 8 -------------------------------- - Density error is +0.000000019403 + Density error is +0.000000197098 - PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.571429 +0.390000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 9 -------------------------------- - Density error is +0.000000001790 + Density error is +0.000000007018 - PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.000000 +0.550000 + LCAO ALGORITHM ------------- MD = 3 ELEC = 10 -------------------------------- - Density error is +0.000000000200 + Density error is +0.000000000786 charge density convergence is achieved - final etot is -219.862372141037 eV + final etot is -219.607783910283 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.14869867 -0.31798991 -0.37001841 + H2 -0.85450265 +0.04119801 -0.00206159 + H3 +0.29971736 +0.54032473 +0.04908535 + H4 +0.13999116 -0.33864187 +0.66575037 + C1 +0.26609546 +0.07510904 -0.34275572 + + + ><><><><><><><><><><><><><><><><><><><><><>< + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.122226 +0.032180 +0.116764 + +0.032180 +1.657347 -0.126403 + +0.116764 -0.126403 +1.723460 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 2 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +2.005975 Kbar +Virial Term is +1.834344 Kbar +Kenetic Term is +0.171631 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.300863 +0.016677 +0.131929 + +0.016677 +1.845488 -0.157565 + +0.131929 -0.157565 +1.871574 + nloc = +289 + searching radius is (Bohr)) = +18.890000 + searching radius unit is (Bohr)) = +1.889726 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 1 -------------------------------- + + Density error is +0.022903825034 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 2 -------------------------------- + + Density error is +0.005231736899 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 3 -------------------------------- + + Density error is +0.002975059067 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 4 -------------------------------- + + Density error is +0.000173879669 + LCAO ALGORITHM ------------- MD = 4 ELEC = 5 -------------------------------- + + Density error is +0.000015476188 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 6 -------------------------------- + + Density error is +0.000002587975 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 7 -------------------------------- + + Density error is +0.000000853005 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 8 -------------------------------- + + Density error is +0.000000222683 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 9 -------------------------------- + + Density error is +0.000000006438 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 10 -------------------------------- + + Density error is +0.000000000469 + + charge density convergence is achieved + final etot is -219.633022026645 eV ><><><><><><><><><><><><><><><><><><><><><>< @@ -593,12 +642,12 @@ Kenetic Term is +0.105188 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 +0.332157 -0.540133 -0.744680 - H2 -0.978294 +0.129701 -0.061949 - H3 +0.426044 +0.880050 -0.050137 - H4 +0.219024 -0.477786 +0.818662 - C1 +0.001069 +0.008168 +0.038104 + atom x y z + H1 -0.08944999 +0.07442795 +0.18000672 + H2 +0.03338775 -0.07984094 +0.07354084 + H3 -0.06629687 -0.21435038 +0.08691687 + H4 -0.06278862 +0.05975732 -0.03768322 + C1 +0.18514773 +0.16000604 -0.30278121 ><><><><><><><><><><><><><><><><><><><><><>< @@ -607,33 +656,33 @@ Kenetic Term is +0.105188 Kbar ><><><><><><><><><><><><><><><><><><><><><>< - +2.479531 -0.031426 -0.026005 - -0.031426 +2.489387 -0.034015 - -0.026005 -0.034015 +2.420180 + -0.221394 +0.045651 +0.032718 + +0.045651 -0.552324 +0.014849 + +0.032718 +0.014849 -0.370471 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 3 + ------------------------------------------- output Pressure for check! -Virtual Pressure is +5.575435 Kbar -Virial Term is +4.926065 Kbar -Kenetic Term is +0.649370 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 3 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.111265 (Rydberg) - NVT Temperature : +1261.973956 (K) - NVT Kinetic energy : +0.047957 (Rydberg) - NVT Potential energy : -16.159581 (Rydberg) - maxForce : +0.000370 - maxStep : +0.117517 - MD_STEP SystemE Conserved DeltaE Temperature - +3 -8.079790 -8.055632 +0.000000 +1447.243804 +Virtual Pressure is -0.295464 Kbar +Virial Term is -0.381396 Kbar +Kenetic Term is +0.085933 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.125999 +0.039645 +0.041658 + +0.039645 -0.463775 +0.000327 + +0.041658 +0.000327 -0.296617 -------------------------------------------- - !FINAL_ETOT_IS -219.8623721410366443 eV + !FINAL_ETOT_IS -219.6330220266447668 eV -------------------------------------------- @@ -642,60 +691,91 @@ Kenetic Term is +0.649370 Kbar |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +75.201 15 +5.01 +100.00 % - Run_pw plane_wave_line +75.18 1 +75.18 +99.97 % - PW_Basis gen_pw +0.28 1 +0.28 +0.37 % - Run_MD_PW md_cells_pw +74.83 1 +74.83 +99.51 % - ppcell_vl init_vloc +3.95 1 +3.95 +5.25 % - Potential init_pot +0.79 4 +0.20 +1.05 % - FFT FFT3D +28.10 8433 +0.00 +37.37 % - Charge atomic_rho +2.57 7 +0.37 +3.42 % - Potential v_of_rho +3.44 34 +0.10 +4.57 % - H_XC_pw v_xc +3.23 37 +0.09 +4.29 % - H_Hartree_pw v_hartree +0.42 34 +0.01 +0.56 % - wavefunc wfcinit +1.09 4 +0.27 +1.45 % - pp_cell_vnl getvnl +0.15 40 +0.00 +0.20 % - Hamilt_PW diagH_subspace +3.43 34 +0.10 +4.56 % - Hamilt_PW h_psi +29.25 3312 +0.01 +38.89 % - Hamilt_PW vloc +26.78 3312 +0.01 +35.61 % - Hamilt_PW vnl +2.38 3312 +0.00 +3.16 % - Hamilt_PW add_nonlocal_pp +1.01 3312 +0.00 +1.34 % - Run_MD_PW md_ions_pw +70.11 1 +70.11 +93.22 % - Electrons self_consistent +60.10 3 +20.03 +79.92 % - Electrons c_bands +31.03 30 +1.03 +41.27 % - Hamilt diagH_pw +30.90 30 +1.03 +41.09 % - Diago_CG diag +27.87 32 +0.87 +37.06 % - Charge sum_band +2.85 30 +0.10 +3.79 % - Charge rho_mpi +1.04 30 +0.03 +1.39 % - Charge mix_rho +0.97 30 +0.03 +1.29 % - Forces cal_force_nl +0.24 3 +0.08 +0.32 % - Stress_PW cal_stress +3.15 3 +1.05 +4.19 % - Stress_Func stress_ew +22.56 2 +11.28 +29.99 % - Force_Func stress_ew +22.55 2 +11.28 +29.99 % - Stress_Func stress_gga +0.13 3 +0.04 +0.17 % - Stress_Func stress_loc +1.37 3 +0.46 +1.82 % - Stress_Func stres_nl +1.54 3 +0.51 +2.05 % + total +62.27030 11 +5.66 +100.00% + Run_lcao lcao_line +62.25252 1 +62.25 +99.97% + PW_Basis gen_pw +0.44186 1 +0.44 +0.71% + PW_complement setup_GVectors +0.13954 10 +0.01 +0.22% + mymath heapsort +0.11428 10 +0.01 +0.18% + PW_Basis setup_struc_factor +0.31476 4 +0.08 +0.51% + ORB_control read_orb_first +0.19407 1 +0.19 +0.31% + LCAO_Orbitals Read_Orbitals +0.19355 1 +0.19 +0.31% + NOrbital_Lm extra_uniform +0.11935 8 +0.01 +0.19% + ORB_control set_orb_tables +1.84065 1 +1.84 +2.96% + ORB_gen_tables gen_tables +1.84031 1 +1.84 +2.96% + ORB_table_phi init_Table +1.13995 1 +1.14 +1.83% + ORB_table_phi cal_ST_Phi12_R +1.04009 126 +0.01 +1.67% + ORB_table_beta init_Table_Beta +0.36249 1 +0.36 +0.58% + ORB_table_beta VNL_PhiBeta_R +0.33539 56 +0.01 +0.54% + ppcell_vl init_vloc +1.44213 1 +1.44 +2.32% + Potential init_pot +2.41092 8 +0.30 +3.87% + Potential set_local_pot +0.12279 8 +0.02 +0.20% + FFT FFT3D +7.96165 742 +0.01 +12.79% + Charge atomic_rho +3.71033 7 +0.53 +5.96% + Potential v_of_rho +10.44195 51 +0.20 +16.77% + XC_Functional v_xc +9.57496 55 +0.17 +15.38% + H_Hartree_pw v_hartree +1.48001 51 +0.03 +2.38% + Run_MD_LCAO opt_ions +57.14849 1 +57.15 +91.77% + NVT_NHC setup +15.41147 1 +15.41 +24.75% + MD_func force_stress +30.72345 2 +15.36 +49.34% + LOOP_elec solve_elec_stru +34.17038 4 +8.54 +54.87% + LOOP_elec set_matrix_grid +0.25548 4 +0.06 +0.41% + Grid_Technique init +0.25436 4 +0.06 +0.41% + Grid_BigCellgrid_expansion_index +0.16191 8 +0.02 +0.26% + LOOP_elec solver +33.91180 4 +8.48 +54.46% + ELEC_scf scf +33.91178 4 +8.48 +54.46% + ELEC_cbands_k cal_bands +12.25275 43 +0.28 +19.68% + Gint_k vlocal +5.51832 43 +0.13 +8.86% + Efficience each_k +6.68896 43 +0.16 +10.74% + Efficience H_k +6.63026 43 +0.15 +10.65% + LCAO_Hamilt calculate_Hk +6.63019 43 +0.15 +10.65% + Gint_k folding_vl_k +6.62916 43 +0.15 +10.65% + Gint_k Distri +6.62844 43 +0.15 +10.64% + Local_Orbital_Cha sum_bands +10.17155 43 +0.24 +16.33% + Gint_k cal_rho_k +4.81788 43 +0.11 +7.74% + Charge mix_rho +2.39378 43 +0.06 +3.84% + Force_Stress_LCAO getForceStress +19.05964 4 +4.76 +30.61% + Forces cal_force_loc +0.15309 4 +0.04 +0.25% + Stress_Func stress_loc +3.00556 4 +0.75 +4.83% + Stress_Func stress_har +0.13717 4 +0.03 +0.22% + Stress_Func stress_gga +0.37225 4 +0.09 +0.60% + Force_LCAO_k ftable_k +7.61660 4 +1.90 +12.23% + Force_LCAO_k cal_fvl_dphi_k +7.59900 4 +1.90 +12.20% + Gint_k svl_k_RealSpace +6.71052 4 +1.68 +10.78% + Gint_k evaluate_vl_force +0.84339 119664 +0.00 +1.35% + Gint_k evaluate_vl_stress +1.55075 119664 +0.00 +2.49% + Gint_k folding_force +3.87680 4 +0.97 +6.23% + MD_func md_force_stress +27.70880 2 +13.85 +44.50% ---------------------------------------------------------------------------------------- CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +71.1170 - Charge_Pulay Rrho +13.1836 - Charge_Pulay dRrho +11.5356 - Charge_Pulay drho +11.5356 - Use_FFT porter +3.2959 - PW_Basis struc_fac +2.6757 - wavefunc evc +2.3411 - Charge rho +1.6479 - Charge rho_save +1.6479 - Charge rho_core +1.6479 - Potential vltot +1.6479 - Potential vr +1.6479 - Potential vr_eff +1.6479 - Potential vr_eff1 +1.6479 - Potential vnew +1.6479 - Charge_Pulay rho_save2 +1.6479 + +1147.8317 + ORB_table_phi Jl(x) +131.0928 + Charge_Pulay Rrho +23.7305 + Charge_Pulay dRrho +20.7642 + Charge_Pulay drho +20.7642 + Use_FFT porter +5.9326 + Grid_Meshcell index2normal +5.2972 + Grid_Meshcell index2ucell +5.2972 + PW_Basis struc_fac +5.1034 + ORB_table_phi Table_SR&TR +3.6736 + Charge rho +2.9663 + Charge rho_save +2.9663 + Charge rho_core +2.9663 + Potential vltot +2.9663 + Potential vr +2.9663 + Potential vr_eff +2.9663 + Potential vr_eff1 +2.9663 + Potential vnew +2.9663 + Charge_Pulay rho_save2 +2.9663 + init_meshball meshball_pos +1.9470 + Charge rhog +1.2758 + Charge rhog_save +1.2758 + Charge kin_r +1.2758 + Charge kin_r_save +1.2758 + Charge rhog_core +1.2758 + ORB_table_beta Table_NR +1.1560 ---------------------------------------------------------- - Start Time : Fri Nov 12 18:16:22 2021 - Finish Time : Fri Nov 12 18:17:37 2021 - Total Time : 0 h 1 mins 15 secs + Start Time : Sun Apr 17 15:11:14 2022 + Finish Time : Sun Apr 17 15:12:16 2022 + Total Time : 0 h 1 mins 2 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU index 07964f6fe..06d2a8533 100644 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU @@ -6,20 +6,27 @@ LATTICE_CONSTANT 1.8897261254578281 LATTICE_VECTORS -9.706914371019787 0.0 0.0 --0.2813826030727322 9.684068712553056 0.0 -0.1582462664821918 -0.16381766835153533 9.582973858264781 +9.37644206717057 0.0 0.0 +-0.014813577222070317 9.326697659660574 0.0 +-0.1523571207181622 -0.1557268613107592 9.522274826700935 ATOMIC_POSITIONS Cartesian # Cartesian(Unit is LATTICE_CONSTANT) H 0.0 4 -5.096428397218 3.892435586573 3.461810245711 1 1 1 -3.799158121761 4.554674552629 4.165563541923 1 1 1 -5.223899470809 5.330330533668 4.211137245440 1 1 1 -5.005416874557 3.981655544542 5.086650081968 1 1 1 +5.112066187378 3.862243345891 3.417909125283 1 1 1 +3.744498473484 4.562973797398 4.166757218402 1 1 1 +5.245366521375 5.379019566172 4.209449753704 1 1 1 +5.018512728297 3.953726845718 5.124105837070 1 1 1 C 0.0 1 -4.779871851926 4.438976241080 4.227727834445 1 1 1 +4.782575995526 4.437421837856 4.229112966039 1 1 1 + +NUMERICAL_ORBITAL +H_gga_8au_60Ry_2s1p.orb +C_gga_8au_60Ry_2s2p1d.orb + +NUMERICAL_DESCRIPTOR +jle.orb diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT deleted file mode 100644 index c3181c397..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT +++ /dev/null @@ -1,20 +0,0 @@ -INPUT_PARAMETERS - -calculation md -atom_file STRU -kpoint_file KPT -pseudo_dir ./ -ntype 2 -symmetry 1 -ecutwfc 90 - -npool 1 - -mixing_type pulay -mixing_beta 0.4 - -nstep 3 -force_thr_ev 0.02 -#move_method cg -out_stru 0 -stress 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT deleted file mode 100644 index 63bd0ed40..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT +++ /dev/null @@ -1,263 +0,0 @@ -INPUT_PARAMETERS -#Parameters (1.General) -suffix ABACUS #the name of main output directory -latname test #the name of lattice name -atom_file STRU #the filename of file containing atom positions -kpoint_file KPT #the name of file containing k points -pseudo_dir .// #the directory containing pseudo files -orbital_dir #the directory containing orbital files -pseudo_type auto #the type pseudo files -pseudo_rcut 15 #cut-off radius for radial integration -renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE -lmaxmax 2 #maximum of l channels used -dft_functional none #exchange correlation functional -calculation md #test; scf; relax; nscf; ienvelope; istate; -ntype 2 #atom species number -nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin -nbands 0 #number of bands -nbands_sto 0 #number of stochastic bands -nbands_istate 5 #number of bands around Fermi level for istate calulation -nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT -symmetry 0 #turn symmetry on or off -set_vel 0 #read velocity from STRU or not -symmetry_prec 1e-05 #accuracy for symmetry -nelec 0 #input number of electrons -tot_magnetization 0 #total magnetization of the system - -#Parameters (2.PW) -ecutwfc 90 ##energy cutoff for wave functions -diago_cg_maxiter 50 #max iteration number for cg -diago_cg_prec 1 #diago_cg_prec -ethr 0.01 #threshold for eigenvalues is cg electron iterations -dr2 1e-09 #charge density error -start_wfc atomic #start wave functions are from 'atomic' or 'file' -start_charge atomic #start charge is from 'atomic' or file -charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA -out_charge 0 #>0 output charge density for selected electron steps -out_potential 0 #output realspace potential -out_wf 0 #output wave functions -out_dos 0 #output energy and dos -out_band 0 #output energy and band structure -restart_save 0 #print to disk every step for restart -restart_load 0 #restart from disk -read_file_dir auto #directory of files for reading -nx 0 #number of points along x axis for FFT grid -ny 0 #number of points along y axis for FFT grid -nz 0 #number of points along z axis for FFT grid -cell_factor 1.2 #used in the construction of the pseudopotential tables - -#Parameters (3.Relaxation) -ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx -niter 40 ##number of electron iterations -force_set 0 #output the force_set or not -nstep 3 #number of ion iteration steps -out_stru 0 #output the structure files after each ion step -force_thr 0.00077787 #force threshold, unit: Ry/Bohr -force_thr_ev 0.02 #force threshold, unit: eV/Angstrom -force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom -cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom -stress_thr 0.01 #stress threshold -press1 0 #target pressure, unit: KBar -press2 0 #target pressure, unit: KBar -press3 0 #target pressure, unit: KBar -bfgs_w1 0.01 #wolfe condition 1 for bfgs -bfgs_w2 0.5 #wolfe condition 2 for bfgs -trust_radius_max 0.8 #maximal trust radius, unit: Bohr -trust_radius_min 1e-05 #minimal trust radius, unit: Bohr -trust_radius_ini 0.5 #initial trust radius, unit: Bohr -stress 1 #calculate the stress or not -fixed_axes None #which axes are fixed -move_method cg #bfgs; sd; cg; cg_bfgs; -out_level m #ie(for electrons); i(for ions); -out_dm 0 #>0 output density matrix -out_descriptor 0 #>0 compute descriptor for deepks -lmax_descriptor 2 #>0 lmax used in descriptor for deepks - -#Parameters (4.LCAO) -basis_type pw #PW; LCAO in pw; LCAO -new_dm 1 #Type of density matrix; 0: old 1: new -search_radius -1 #input search radius (Bohr) -search_pbc 1 #input periodic boundary condition -lcao_ecut 0 #energy cutoff for LCAO -lcao_dk 0.01 #delta k for 1D integration in LCAO -lcao_dr 0.01 #delta r for 1D integration in LCAO -lcao_rmax 30 #max R for 1D two-center integration table -out_hs 0 #output H and S matrix -out_hs2 0 #output H(R) and S(R) matrix -out_r 0 #output r(R) matrix -out_lowf 0 #ouput LCAO wave functions -bx 1 #division of an element grid in FFT grid along x -by 1 #division of an element grid in FFT grid along y -bz 1 #division of an element grid in FFT grid along z - -#Parameters (5.Smearing) -smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv -sigma 0.01 #energy range for smearing - -#Parameters (6.Charge Mixing) -mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden -mixing_beta 0.4 #mixing parameter: 0 means no new charge -mixing_ndim 8 #mixing dimension in pulay -mixing_gg0 0 #mixing parameter in kerker - -#Parameters (7.DOS) -dos_emin_ev -15 #minimal range for dos -dos_emax_ev 15 #maximal range for dos -dos_edelta_ev 0.01 #delta energy for dos -dos_scale 0.01 #scale dos range by -dos_sigma 0.07 #gauss b coefficeinet(default=0.07) - -#Parameters (8.Technique) -gamma_only 0 #gamma only, only used in LCAO basis -diago_proc 8 #number of proc used to diago -npool 1 #number of pools for k points, pw only -mem_saver 0 #memory saver for many k points used -printe 100 #print band energy for selectively ionic steps - -#Parameters (9.SIAO) -selinv_npole 40 #number of selected poles -selinv_temp 2000 #temperature for Fermi-Dirac distribution -selinv_gap 0 #supposed gap in the calculation -selinv_deltae 2 #expected energy range -selinv_mu -1 #chosen mu as Fermi energy -selinv_threshold 0.001 #threshold for calculated electron number -selinv_niter 50 #max number of steps to update mu - -#Parameters (10.Molecular dynamics) -md_mdtype 1 #choose ensemble -md_potential FP #choose potential -md_dt 1 #time step -mnhc 4 #number of Nose-Hoover chains -md_qmass 1 #mass of thermostat -md_tfirst 0 #temperature first -md_tlast 0 #temperature last -md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD -md_mdoutpath mdoutput #output path of md -md_rstmd 0 #whether restart -md_fixtemperature 1 #period to change temperature -md_ediff 0.0001 #parameter for constraining total energy change -md_ediffg 0.001 #parameter for constraining max force change -NVT_tau 0 #parameter for adjust effect of thermostat -NVT_control 1 #choose which thermostat used in NVT ensemble -rcut_lj 8.5 #cutoff radius of LJ potential -epsilon_lj 0.01032 #the value of epsilon for LJ potential -sigma_lj 3.405 #the value of sigma for LJ potential - -#Parameters (11.Efield) -efield 0 #add electric field -edir 1 #add electric field -emaxpos 0.5 #maximal position of efield [0,1) -eopreg 0.1 #where sawlike potential decrease -eamp 0.001 #amplitute of the efield, unit is a.u. -eamp_v 0.05144 #amplitute of the efield, unit is V/A - -#Parameters (12.Test) -out_alllog 0 #output information for each processor, when parallel -nurse 0 #for coders -colour 0 #for coders, make their live colourful -t_in_h 1 #calculate the kinetic energy or not -vl_in_h 1 #calculate the local potential or not -vnl_in_h 1 #calculate the nonlocal potential or not -vh_in_h 1 #calculate the hartree potential or not -vxc_in_h 1 #calculate the xc potential or not -vion_in_h 1 #calculate the local ionic potential or not -test_force 0 #test the force -test_stress 0 #test the force - -#Parameters (13.Other Methods) -mlwf_flag 0 #turn MLWF on or off -opt_epsilon2 0 #calculate the dielectic function -opt_nbands 0 #number of bands for optical calculation - -#Parameters (14.VdW Correction) -vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj -vdw_s6 default #scale parameter of d2/d3_0/d3_bj -vdw_s8 default #scale parameter of d3_0/d3_bj -vdw_a1 default #damping parameter of d3_0/d3_bj -vdw_a2 default #damping parameter of d3_bj -vdw_d 20 #damping parameter of d2 -vdw_abc 0 #third-order term? -vdw_C6_file default #filename of C6 -vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 -vdw_R0_file default #filename of R0 -vdw_R0_unit A #unit of R0, A or Bohr -vdw_model radius #expression model of periodic structure, radius or period -vdw_radius default #radius cutoff for periodic structure -vdw_radius_unit Bohr #unit of radius cutoff for periodic structure -vdw_cn_thr 40 #radius cutoff for cn -vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom -vdw_period 3 3 3 #periods of periodic structure - -#Parameters (15.spectrum) -spectral_type None #the type of the calculated spectrum -spectral_method 0 #0: tddft(linear response) -kernel_type rpa #the kernel type: rpa, tdlda ... -eels_method 0 #0: hilbert_transform method; 1: standard method -absorption_method 0 #0: vasp's method 1: pwscf's method -system bulk #the calculate system -eta 0.05 #eta(Ry) -domega 0.01 #domega(Ry) -nomega 300 #nomega -ecut_chi 1 #the dimension of chi matrix -q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate -q_direction 1 0 0 #the q direction -nq 1 #the total number of qpoints for calculation -out_epsilon 1 #output epsilon or not -out_chi 0 #output chi or not -out_chi0 0 #output chi0 or not -fermi_level 0 #the change of the fermi_level(Ry) -coulomb_cutoff 0 # turn on the coulomb_cutoff or not -kmesh_interpolation 0 #calculting -qcar 0 0 0 #(unit: 2PI/lat0) -ocp 0 #change occupation or not -ocp_set none #set occupation -lcao_box 10 10 10 #the scale for searching the existence of the overlap - mulliken 0 # mulliken charge or not -intrasmear 0 #Eta -shift 0 #shift -metalcalc 0 #metal or not -eps_degauss 0.01 #degauss in calculating epsilon0 -noncolin 0 #using non-collinear-spin -lspinorb 0 #consider the spin-orbit interaction - -#Parameters (17.exx) -exx_hybrid_type no #no, hf, pbe0, hse or opt_orb -exx_hybrid_alpha 0.25 # -exx_hse_omega 0.11 # -exx_separate_loop 1 #0 or 1 -exx_hybrid_step 100 # -exx_lambda 0.3 # -exx_pca_threshold 0 # -exx_c_threshold 0 # -exx_v_threshold 0 # -exx_dm_threshold 0 # -exx_schwarz_threshold0 # -exx_cauchy_threshold0 # -exx_ccp_threshold 1e-08 # -exx_ccp_rmesh_times 10 # -exx_distribute_type htime #htime or kmeans1 or kmeans2 -exx_opt_orb_lmax 0 # -exx_opt_orb_ecut 0 # -exx_opt_orb_tolerence0 # - -#Parameters (17.tddft) -tddft 0 #calculate tddft or not -td_dr2 1e-09 #threshold for electronic iteration of tddft -td_dt 0.02 #time of ion step -td_force_dt 0.02 #time of force change -td_val_elec_01 1 #td_val_elec_01 -td_val_elec_02 1 #td_val_elec_02 -td_val_elec_03 1 #td_val_elec_03 -td_vext 0 #add extern potential or not -td_vext_dire 1 #extern potential direction -td_timescale 0.5 #extern potential td_timescale -td_vexttype 1 #extern potential type -td_vextout 0 #output extern potential or not -td_dipoleout 0 #output dipole or not - -#Parameters (18.berry_wannier) -berry_phase 0 #calculate berry phase or not -gdir 3 #calculate the polarization in the direction of the lattice std::vector -towannier90 0 #use wannier90 code interface or not -nnkpfile seedname.nnkp #the wannier90 code nnkp file name -wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD deleted file mode 100644 index f42357382..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD +++ /dev/null @@ -1,27 +0,0 @@ -ATOMIC_SPECIES -H 1.008 H_ONCV_PBE-1.0.upf -C 12.01 C_ONCV_PBE-1.0.upf - -LATTICE_CONSTANT -1.88972612546 - -LATTICE_VECTORS -9.27069258481 0 0 #latvec1 -0.0128238456952 9.56209520274 0 #latvec2 -0.169560774735 -0.0300305282636 9.58609795568 #latvec3 - -ATOMIC_POSITIONS -Direct - -H #label -0 #magnetism -4 #number of atoms -0.547461705223 0.400166750312 0.349585199322 1 1 1 0 0 0 -0.387154932277 0.478943964961 0.433851040704 1 1 1 0 0 0 -0.560703231408 0.571623190735 0.438580636423 1 1 1 0 0 0 -0.532932139137 0.411873023092 0.541312594704 1 1 1 0 0 0 - -C #label -0 #magnetism -1 #number of atoms -0.507726212428 0.465642779417 0.440714011322 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif deleted file mode 100644 index 6d8352991..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.27069 -_cell_length_b 9.5621 -_cell_length_c 9.58764 -_cell_angle_alpha 90.1781 -_cell_angle_beta 88.9867 -_cell_angle_gamma 89.9232 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.542192 0.408202 0.360768 -H 0.401673 0.477208 0.434698 -H 0.554241 0.559124 0.439031 -H 0.529933 0.417895 0.530426 -C 0.507735 0.465662 0.44058 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif deleted file mode 100644 index bd632634b..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.27069 -_cell_length_b 9.5621 -_cell_length_c 9.58764 -_cell_angle_alpha 90.1781 -_cell_angle_beta 88.9867 -_cell_angle_gamma 89.9232 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.543005 0.406936 0.359006 -H 0.399395 0.477474 0.434569 -H 0.555241 0.561082 0.43897 -H 0.530384 0.416975 0.532107 -C 0.507737 0.465659 0.440603 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif deleted file mode 100644 index 724fd225e..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.27069 -_cell_length_b 9.5621 -_cell_length_c 9.58764 -_cell_angle_alpha 90.1781 -_cell_angle_beta 88.9867 -_cell_angle_gamma 89.9232 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.545037 0.403807 0.354649 -H 0.393743 0.47814 0.434243 -H 0.55774 0.565945 0.438806 -H 0.53153 0.414656 0.536324 -C 0.507736 0.465651 0.440656 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif deleted file mode 100644 index 659d52e66..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 9.27069 -_cell_length_b 9.5621 -_cell_length_c 9.58764 -_cell_angle_alpha 90.1781 -_cell_angle_beta 88.9867 -_cell_angle_gamma 89.9232 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -H 0.547462 0.400167 0.349585 -H 0.387155 0.478944 0.433851 -H 0.560703 0.571623 0.438581 -H 0.532932 0.411873 0.541313 -C 0.507726 0.465643 0.440714 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log deleted file mode 100644 index 2a1ad64a8..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log +++ /dev/null @@ -1,701 +0,0 @@ - - WELCOME TO ABACUS - - 'Atomic-orbital Based Ab-initio Computation at UStc' - - Website: http://abacus.ustc.edu.cn/ - - Version: Parallel, in development - Processor Number is 8 - Start Time is Fri Nov 12 18:17:38 2021 - - ------------------------------------------------------------------------------------ - - READING GENERAL INFORMATION - global_out_dir = OUT.ABACUS/ - global_in_card = INPUT - pseudo_dir = - orbital_dir = - pseudo_type = auto - DRANK = 1 - DSIZE = 8 - DCOLOR = 1 - GRANK = 1 - GSIZE = 1 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Reading atom information in unitcell: | - | From the input file and the structure file we know the number of | - | different elments in this unitcell, then we list the detail | - | information for each element, especially the zeta and polar atomic | - | orbital number for each element. The total atom number is counted. | - | We calculate the nearest atom distance for each atom and show the | - | Cartesian and Direct coordinates for each atom. We list the file | - | address for atomic orbitals. The volume and the lattice vectors | - | in real and reciprocal space is also shown. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - READING UNITCELL INFORMATION - ntype = 2 - atom label for species 1 = H - atom label for species 2 = C - lattice constant (Bohr) = 1.88973 - lattice constant (Angstrom) = 1 - - READING ATOM TYPE 1 - atom label = H - L=0, number of zeta = 1 - L=1, number of zeta = 1 - L=2, number of zeta = 1 - number of atom for this type = 4 - start magnetization = FALSE - start magnetization = FALSE - start magnetization = FALSE - start magnetization = FALSE - - READING ATOM TYPE 2 - atom label = C - L=0, number of zeta = 1 - L=1, number of zeta = 1 - L=2, number of zeta = 1 - number of atom for this type = 1 - start magnetization = FALSE - - TOTAL ATOM NUMBER = 5 - - CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). - atom x y z mag vx vy vz - tauc_H1 5.09290605164 3.89242871555 3.45835777937 0 0 0 0 - tauc_H2 3.80361094208 4.55005711875 4.16705754763 0 0 0 0 - tauc_H3 5.21981288147 5.33321039636 4.20859510266 0 0 0 0 - tauc_H4 5.00814830724 3.9800234484 5.08471194545 0 0 0 0 - tauc_C1 4.78773457902 4.43947390549 4.22344175994 0 0 0 0 - - - Volume (Bohr^3) = 5734.60762332 - Volume (A^3) = 849.780160031 - - Lattice vectors: (Cartesian coordinate: in unit of a_0) - +9.27069258481 +0 +0 - +0.0128238456952 +9.56209520274 +0 - +0.169560774735 -0.0300305282636 +9.58609795568 - Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) - +0.107866806158 -0.000144661525376 -0.001908422339 - -0 +0.104579590435 +0.000327618219725 - +0 +0 +0.104317732264 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Reading pseudopotentials files: | - | The pseudopotential file is in UPF format. The 'NC' indicates that | - | the type of pseudopotential is 'norm conserving'. Functional of | - | exchange and correlation is decided by 4 given parameters in UPF | - | file. We also read in the 'core correction' if there exists. | - | Also we can read the valence electrons number and the maximal | - | angular momentum used in this pseudopotential. We also read in the | - | trail wave function, trail atomic density and local-pseudopotential| - | on logrithmic grid. The non-local pseudopotential projector is also| - | read in if there is any. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - PAO radial cut off (Bohr) = 15 - - Read in pseudopotential file is H_ONCV_PBE-1.0.upf - pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = - nonlocal core correction = 0 - valence electrons = 1 - lmax = 0 - number of zeta = 0 - number of projectors = 2 - L of projector = 0 - L of projector = 0 - PAO radial cut off (Bohr) = 15 - - Read in pseudopotential file is C_ONCV_PBE-1.0.upf - pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = - nonlocal core correction = 0 - valence electrons = 4 - lmax = 1 - number of zeta = 0 - number of projectors = 4 - L of projector = 0 - L of projector = 0 - L of projector = 1 - L of projector = 1 - initial pseudo atomic orbital number = 0 - NLOCAL = 45 - - SETUP THE ELECTRONS NUMBER - electron number of element H = 1 - total electron number of element H = 4 - electron number of element C = 4 - total electron number of element C = 4 - occupied bands = 4 - NBANDS = 14 - DONE : SETUP UNITCELL Time : 0.0822040801286 (SEC) - - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Setup K-points | - | We setup the k-points according to input parameters. | - | The reduced k-points are set according to symmetry operations. | - | We treat the spin as another set of k-points. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - - SETUP K-POINTS - nspin = 1 - Input type of k points = Monkhorst-Pack(Gamma) - nkstot = 1 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 1 - - k-point number in this process = 1 - minimum distributed K point number = 1 - - KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT - 1 0 0 0 2 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 2 - DONE : INIT K-POINTS Time : 0.0836835908704 (SEC) - - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Setup plane waves: | - | Use the energy cutoff and the lattice vectors to generate the | - | dimensions of FFT grid. The number of FFT grid on each processor | - | is 'nrxx'. The number of plane wave basis in reciprocal space is | - | different for charege/potential and wave functions. We also set | - | the 'sticks' for the parallel of FFT. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - - SETUP THE PLANE WAVE BASIS - energy cutoff for wavefunc (unit:Ry) = 90 - [fft grid for wave functions] = 108, 120, 120 - [fft grid for charge/potential] = 108, 120, 120 - [fft grid division] = 1, 1, 1 - [big fft grid for charge/potential] = 108, 120, 120 - nbxx = 194400 - nrxx = 194400 - - SETUP PLANE WAVES FOR CHARGE/POTENTIAL - number of plane waves = 661353 - number of sticks = 9057 - - SETUP PLANE WAVES FOR WAVE FUNCTIONS - number of plane waves = 82689 - number of sticks = 2267 - - PARALLEL PW FOR CHARGE/POTENTIAL - PROC COLUMNS(POT) PW - 1 1132 82670 - 2 1132 82669 - 3 1132 82669 - 4 1132 82669 - 5 1132 82669 - 6 1132 82669 - 7 1133 82669 - 8 1132 82669 - --------------- sum ------------------- - 8 9057 661353 - - PARALLEL PW FOR WAVE FUNCTIONS - PROC COLUMNS(W) PW - 1 284 10334 - 2 283 10336 - 3 283 10338 - 4 281 10335 - 5 285 10338 - 6 285 10336 - 7 282 10334 - 8 284 10338 - --------------- sum ------------------- - 8 2267 82689 - - SETUP COORDINATES OF PLANE WAVES - number of total plane waves = 661353 - - SETUP COORDINATES OF PLANE WAVES - number of |g| = 79694 - max |g| = 32.5641662388 - min |g| = 0 - DONE : INIT PLANEWAVE Time : 0.336783995619 (SEC) - - npwx = 10334 - - SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS - H non-local projectors: - projector 1 L=0 - projector 2 L=0 - C non-local projectors: - projector 1 L=0 - projector 2 L=0 - projector 3 L=1 - projector 4 L=1 - TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 - DONE : LOCAL POTENTIAL Time : 4.04769805988 (SEC) - - - Init Non-Local PseudoPotential table : - Init Non-Local-Pseudopotential done. - DONE : NON-LOCAL POTENTIAL Time : 4.05365722452 (SEC) - - start_pot = atomic - DONE : INIT POTENTIAL Time : 4.48892 (SEC) - - - Make real space PAO into reciprocal space. - max mesh points in Pseudopotential = 601 - dq(describe PAO in reciprocal space) = 0.01 - max q = 1143 - - number of pseudo atomic orbitals for H is 0 - - number of pseudo atomic orbitals for C is 0 - DONE : INIT BASIS Time : 4.74304 (SEC) - - ...............Nose-Hoover Chain parameter initialization............... - Temperature = 0 - Temperature2 = 0 - NHC frequency = 0.00120944 - NHC chain = 4 - Qmass = 1822.89 - ............................................................... - - PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - K-point CG iter num Time(Sec) - 1 10.000000 1.100000 - - Density error is 0.960510453558 - - PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - K-point CG iter num Time(Sec) - 1 2.285714 0.310000 - - Density error is 0.098733734228 - - PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - K-point CG iter num Time(Sec) - 1 4.071429 0.500000 - - Density error is 0.029156016548 - - PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - K-point CG iter num Time(Sec) - 1 3.714286 0.450000 - - Density error is 0.157357850345 - - PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - K-point CG iter num Time(Sec) - 1 3.142857 0.390000 - - Density error is 0.000022976111 - - PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - K-point CG iter num Time(Sec) - 1 8.785714 0.970000 - - Density error is 0.000027903812 - - PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - K-point CG iter num Time(Sec) - 1 4.357143 0.530000 - - Density error is 0.000007318066 - - PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - K-point CG iter num Time(Sec) - 1 5.000000 0.590000 - - Density error is 0.000000148874 - - PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- - K-point CG iter num Time(Sec) - 1 6.428571 0.730000 - - Density error is 0.000000001372 - - PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- - K-point CG iter num Time(Sec) - 1 7.714286 0.860000 - - Density error is 0.000000001003 - - PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- - K-point CG iter num Time(Sec) - 1 7.785714 0.880000 - - Density error is 0.000000000059 - - charge density convergence is achieved - final etot is -219.118728218927 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 +1.508322 -2.517782 -3.530747 - H2 -4.418462 +0.530736 -0.259007 - H3 +1.940423 +3.914120 -0.121649 - H4 +0.930235 -1.848593 +3.369226 - C1 +0.039482 -0.078480 +0.542177 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +11.019212 -0.012921 -0.249753 - -0.012921 +10.888803 +0.464085 - -0.249753 +0.464085 +10.579625 - -output Pressure for check! -Virtual Pressure is +21.658426 Kbar -Virial Term is +21.658426 Kbar -Kenetic Term is +0.000000 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 1 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.104924 (Rydberg) - NVT Temperature : +0.000000 (K) - NVT Kinetic energy : +0.000000 (Rydberg) - NVT Potential energy : -16.104924 (Rydberg) - maxForce : +0.007972 - maxStep : +0.041509 - MD_STEP SystemE Conserved DeltaE Temperature - +1 -8.052462 -8.052462 +0.000000 +175.027577 - - PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +55.142857 +5.680000 - - Density error is +0.003488598323 - - PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.300000 - - Density error is +0.000064088512 - - PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.071429 +0.480000 - - Density error is +0.000016147980 - - PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.214286 +0.410000 - - Density error is +0.000001278683 - - PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.071429 +0.600000 - - Density error is +0.000000184850 - - PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.214286 +0.410000 - - Density error is +0.000000013531 - - PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.285714 +0.610000 - - Density error is +0.000000010165 - - PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.290000 - - Density error is +0.000000003623 - - PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.928571 +0.370000 - - Density error is +0.000000000004 - - charge density convergence is achieved - final etot is -219.434191715312 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 +1.133157 -1.856662 -2.608308 - H2 -3.288841 +0.401876 -0.196306 - H3 +1.454909 +2.915560 -0.103398 - H4 +0.716634 -1.407419 +2.547272 - C1 -0.015860 -0.053356 +0.360740 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +8.401340 -0.025640 -0.170148 - -0.025640 +8.286073 +0.280673 - -0.170148 +0.280673 +8.068639 - -output Pressure for check! -Virtual Pressure is +16.617778 Kbar -Virial Term is +16.504034 Kbar -Kenetic Term is +0.113744 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 2 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.107810 (Rydberg) - NVT Temperature : +533.989848 (K) - NVT Kinetic energy : +0.020293 (Rydberg) - NVT Potential energy : -16.128110 (Rydberg) - maxForce : +0.004362 - maxStep : +0.102614 - MD_STEP SystemE Conserved DeltaE Temperature - +2 -8.064055 -8.053905 +0.000000 +1078.821137 - - PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +53.785714 +5.530000 - - Density error is +0.019612648889 - - PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.300000 - - Density error is +0.000290072895 - - PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.142857 +0.490000 - - Density error is +0.000099169017 - - PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.714286 +0.350000 - - Density error is +0.000008092362 - - PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.428571 +0.530000 - - Density error is +0.000001211193 - - PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.357143 +0.420000 - - Density error is +0.000000051304 - - PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- - K-point CG iter num Time(Sec) - +1 +5.500000 +0.630000 - - Density error is +0.000000007503 - - PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.857143 +0.580000 - - Density error is +0.000000014633 - - PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.214286 +0.300000 - - Density error is +0.000000002243 - - PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- - K-point CG iter num Time(Sec) - +1 +4.142857 +0.500000 - - Density error is +0.000000000398 - - charge density convergence is achieved - final etot is -219.861273145100 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 +0.370637 -0.522900 -0.745579 - H2 -0.985036 +0.136881 -0.067108 - H3 +0.457129 +0.867257 -0.061860 - H4 +0.261706 -0.471416 +0.808625 - C1 -0.104436 -0.009822 +0.065922 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +2.700073 -0.048954 -0.024676 - -0.048954 +2.601966 -0.047102 - -0.024676 -0.047102 +2.553528 - -output Pressure for check! -Virtual Pressure is +5.938130 Kbar -Virial Term is +5.237045 Kbar -Kenetic Term is +0.701085 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 3 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -16.110343 (Rydberg) - NVT Temperature : +1283.993234 (K) - NVT Kinetic energy : +0.048794 (Rydberg) - NVT Potential energy : -16.159500 (Rydberg) - maxForce : +0.000376 - maxStep : +0.119327 - MD_STEP SystemE Conserved DeltaE Temperature - +3 -8.079750 -8.055171 +0.000000 +1471.487172 - - - -------------------------------------------- - !FINAL_ETOT_IS -219.8612731451002276 eV - -------------------------------------------- - - - - - - - |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +68.402 15 +4.56 +100.00 % - Run_pw plane_wave_line +68.38 1 +68.38 +99.97 % - PW_Basis gen_pw +0.25 1 +0.25 +0.37 % - Run_MD_PW md_cells_pw +68.05 1 +68.05 +99.48 % - ppcell_vl init_vloc +3.69 1 +3.69 +5.39 % - Potential init_pot +0.71 4 +0.18 +1.04 % - FFT FFT3D +23.26 8449 +0.00 +34.00 % - Charge atomic_rho +2.26 7 +0.32 +3.31 % - Potential v_of_rho +3.00 34 +0.09 +4.38 % - H_XC_pw v_xc +2.82 37 +0.08 +4.13 % - H_Hartree_pw v_hartree +0.36 34 +0.01 +0.53 % - wavefunc wfcinit +0.99 4 +0.25 +1.44 % - pp_cell_vnl getvnl +0.14 40 +0.00 +0.20 % - Hamilt_PW diagH_subspace +2.84 34 +0.08 +4.15 % - Hamilt_PW h_psi +24.69 3320 +0.01 +36.09 % - Hamilt_PW vloc +22.48 3320 +0.01 +32.86 % - Hamilt_PW vnl +2.12 3320 +0.00 +3.10 % - Hamilt_PW add_nonlocal_pp +0.94 3320 +0.00 +1.37 % - Run_MD_PW md_ions_pw +63.66 1 +63.66 +93.06 % - Electrons self_consistent +54.24 3 +18.08 +79.30 % - Electrons c_bands +26.27 30 +0.88 +38.41 % - Hamilt diagH_pw +26.15 30 +0.87 +38.23 % - Diago_CG diag +23.65 32 +0.74 +34.57 % - Charge sum_band +2.40 30 +0.08 +3.50 % - Charge rho_mpi +0.91 30 +0.03 +1.33 % - Charge mix_rho +0.81 30 +0.03 +1.18 % - Forces cal_force_nl +0.22 3 +0.07 +0.33 % - Stress_PW cal_stress +3.14 3 +1.05 +4.59 % - Stress_Func stress_ew +20.85 2 +10.42 +30.48 % - Force_Func stress_ew +20.85 2 +10.42 +30.48 % - Stress_Func stress_gga +0.12 3 +0.04 +0.17 % - Stress_Func stress_loc +1.30 3 +0.43 +1.91 % - Stress_Func stres_nl +1.62 3 +0.54 +2.36 % - ---------------------------------------------------------------------------------------- - - CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +64.7285 - Charge_Pulay Rrho +11.8652 - Charge_Pulay dRrho +10.3821 - Charge_Pulay drho +10.3821 - Use_FFT porter +2.9663 - PW_Basis struc_fac +2.5229 - wavefunc evc +2.2076 - Charge rho +1.4832 - Charge rho_save +1.4832 - Charge rho_core +1.4832 - Potential vltot +1.4832 - Potential vr +1.4832 - Potential vr_eff +1.4832 - Potential vr_eff1 +1.4832 - Potential vnew +1.4832 - Charge_Pulay rho_save2 +1.4832 - ---------------------------------------------------------- - - Start Time : Fri Nov 12 18:17:38 2021 - Finish Time : Fri Nov 12 18:18:46 2021 - Total Time : 0 h 1 mins 8 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU deleted file mode 100644 index 8bc79faf7..000000000 --- a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU +++ /dev/null @@ -1,25 +0,0 @@ -ATOMIC_SPECIES -H 1.008 H_ONCV_PBE-1.0.upf -C 12.010 C_ONCV_PBE-1.0.upf - -LATTICE_CONSTANT -1.8897261254578281 - -LATTICE_VECTORS -9.270692584805424 0.0 0.0 -0.01282384569524753 9.562095202737858 0.0 -0.16956077473517553 -0.030030528263640357 9.586097955682344 - -ATOMIC_POSITIONS -Cartesian # Cartesian(Unit is LATTICE_CONSTANT) -H -0.0 -4 -5.092906051636 3.892428715541 3.458357779363 1 1 1 -3.803610942086 4.550057118756 4.167057547630 1 1 1 -5.219812881472 5.333210396361 4.208595102670 1 1 1 -5.008148307232 3.980023448407 5.084711945455 1 1 1 -C -0.0 -1 -4.787734579020 4.439473905493 4.223441759937 1 1 1 diff --git a/tests/data/test_coll_abacus.py b/tests/data/test_coll_abacus.py index 6a73b7233..feabec88d 100644 --- a/tests/data/test_coll_abacus.py +++ b/tests/data/test_coll_abacus.py @@ -19,11 +19,11 @@ def setUp(self): if os.path.isdir(self.odir) : shutil.rmtree(self.odir) shutil.copytree('out_data_02_md_abacus', self.odir) - self.ref_coord = np.reshape(np.genfromtxt("abacus.out/coord.raw"), [9, 5, 3]) - self.ref_cell = np.reshape(np.genfromtxt("abacus.out/box.raw"), [9, 3, 3]) - self.ref_e = np.reshape(np.genfromtxt("abacus.out/energy.raw"), [9, ]) - self.ref_f = np.reshape(np.genfromtxt("abacus.out/force.raw"), [9, 5, 3]) - self.ref_v = np.reshape(np.genfromtxt("abacus.out/virial.raw"), [9, 3, 3]) + self.ref_coord = np.reshape(np.genfromtxt("abacus.out/coord.raw"), [8, 5, 3]) + self.ref_cell = np.reshape(np.genfromtxt("abacus.out/box.raw"), [8, 3, 3]) + self.ref_e = np.reshape(np.genfromtxt("abacus.out/energy.raw"), [8, ]) + self.ref_f = np.reshape(np.genfromtxt("abacus.out/force.raw"), [8, 5, 3]) + self.ref_v = np.reshape(np.genfromtxt("abacus.out/virial.raw"), [8, 3, 3]) def tearDown(self): #print("escape.") shutil.rmtree(self.odir) @@ -37,18 +37,18 @@ def test_coll(self): coll_abacus_md(jdata) sys = dpdata.LabeledSystem(self.odir + '/02.md/sys-0004-0001/deepmd//', fmt = 'deepmd/raw') - self.assertEqual(sys.get_nframes(), 9) + self.assertEqual(sys.get_nframes(), 8) - for ff in range(9) : + for ff in range(8) : self.assertAlmostEqual(self.ref_e[ff], sys.data['energies'][ff]) - for ff in range(9) : + for ff in range(8) : for ii in range(5) : for dd in range(3) : self.assertAlmostEqual(self.ref_coord[ff][ii][dd], sys.data['coords'][ff][ii][dd]) self.assertAlmostEqual(self.ref_f[ff][ii][dd], sys.data['forces'][ff][ii][dd]) - for ff in range(9): + for ff in range(8): for ii in range(3) : for jj in range(3) : self.assertAlmostEqual(self.ref_v[ff][ii][jj], diff --git a/tests/generator/param-methane-abacus.json b/tests/generator/param-methane-abacus.json index ab8c4d34e..e9fb42cff 100644 --- a/tests/generator/param-methane-abacus.json +++ b/tests/generator/param-methane-abacus.json @@ -133,7 +133,6 @@ "fp_pp_path": ".", "fp_pp_files": [ "./H_HSCV_PBE-1.0.UPF","./C_HSCV_PBE-1.0.UPF"], "user_fp_params":{ - "lattice_constant":1, "ntype": 2, "ecutwfc": 80, "dr2": 1e-7, diff --git a/tests/generator/test_make_fp.py b/tests/generator/test_make_fp.py index 8158888f8..f706d8ea4 100644 --- a/tests/generator/test_make_fp.py +++ b/tests/generator/test_make_fp.py @@ -156,8 +156,8 @@ dr2 1.000000e-07\n\ niter 50\n\ basis_type pw\n\ -dft_functional pbe\n\ gamma_only 1\n\ +dft_functional pbe\n\ mixing_type pulay\n\ mixing_beta 0.400000\n\ symmetry 1\n\