diff --git a/dpgen/auto_test/Gamma.py b/dpgen/auto_test/Gamma.py new file mode 100644 index 000000000..970146bc2 --- /dev/null +++ b/dpgen/auto_test/Gamma.py @@ -0,0 +1,384 @@ +import glob +import json +import os +import re + +import numpy as np +from monty.serialization import loadfn, dumpfn +from pymatgen.core.structure import Structure +from pymatgen.core.surface import SlabGenerator +from pymatgen.io.ase import AseAtomsAdaptor +from ase.lattice.cubic import BodyCenteredCubic as bcc +from ase.lattice.cubic import FaceCenteredCubic as fcc +from ase.lattice.hexagonal import HexagonalClosedPacked as hcp + +import dpgen.auto_test.lib.vasp as vasp +from dpgen import dlog +from dpgen.auto_test.Property import Property +from dpgen.auto_test.refine import make_refine +from dpgen.auto_test.reproduce import make_repro +from dpgen.auto_test.reproduce import post_repro + + +class Gamma(Property): + """ + Calculation of common gamma lines for bcc and fcc + """ + def __init__(self, + parameter): + parameter['reproduce'] = parameter.get('reproduce', False) + self.reprod = parameter['reproduce'] + if not self.reprod: + if not ('init_from_suffix' in parameter and 'output_suffix' in parameter): + self.miller_index = parameter['miller_index'] + self.displace_direction = parameter['displace_direction'] + self.lattice_type = parameter['lattice_type'] + parameter['supercell_size'] = parameter.get('supercell_size', (1,1,5)) + self.supercell_size = parameter['supercell_size'] + parameter['min_vacuum_size'] = parameter.get('min_vacuum_size', 20) + self.min_vacuum_size = parameter['min_vacuum_size'] + parameter['add_fix'] = parameter.get('add_fix', ['true','true','false']) # standard method + self.add_fix = parameter['add_fix'] + parameter['n_steps'] = parameter.get('n_steps', 10) + self.n_steps = parameter['n_steps'] + self.atom_num = None + parameter['cal_type'] = parameter.get('cal_type', 'relaxation') + self.cal_type = parameter['cal_type'] + default_cal_setting = {"relax_pos": True, + "relax_shape": False, + "relax_vol": False} + if 'cal_setting' not in parameter: + parameter['cal_setting'] = default_cal_setting + else: + if "relax_pos" not in parameter['cal_setting']: + parameter['cal_setting']['relax_pos'] = default_cal_setting['relax_pos'] + if "relax_shape" not in parameter['cal_setting']: + parameter['cal_setting']['relax_shape'] = default_cal_setting['relax_shape'] + if "relax_vol" not in parameter['cal_setting']: + parameter['cal_setting']['relax_vol'] = default_cal_setting['relax_vol'] + self.cal_setting = parameter['cal_setting'] + else: + parameter['cal_type'] = 'static' + self.cal_type = parameter['cal_type'] + default_cal_setting = {"relax_pos": False, + "relax_shape": False, + "relax_vol": False} + if 'cal_setting' not in parameter: + parameter['cal_setting'] = default_cal_setting + else: + if "relax_pos" not in parameter['cal_setting']: + parameter['cal_setting']['relax_pos'] = default_cal_setting['relax_pos'] + if "relax_shape" not in parameter['cal_setting']: + parameter['cal_setting']['relax_shape'] = default_cal_setting['relax_shape'] + if "relax_vol" not in parameter['cal_setting']: + parameter['cal_setting']['relax_vol'] = default_cal_setting['relax_vol'] + self.cal_setting = parameter['cal_setting'] + parameter['init_from_suffix'] = parameter.get('init_from_suffix', '00') + self.init_from_suffix = parameter['init_from_suffix'] + self.parameter = parameter + + def make_confs(self, + path_to_work, + path_to_equi, + refine=False): + path_to_work = os.path.abspath(path_to_work) + if os.path.exists(path_to_work): + dlog.warning('%s already exists' % path_to_work) + else: + os.makedirs(path_to_work) + path_to_equi = os.path.abspath(path_to_equi) + if 'start_confs_path' in self.parameter and os.path.exists(self.parameter['start_confs_path']): + init_path_list = glob.glob(os.path.join(self.parameter['start_confs_path'], '*')) + struct_init_name_list = [] + for ii in init_path_list: + struct_init_name_list.append(ii.split('/')[-1]) + struct_output_name = path_to_work.split('/')[-2] + assert struct_output_name in struct_init_name_list + path_to_equi = os.path.abspath(os.path.join(self.parameter['start_confs_path'], + struct_output_name, 'relaxation', 'relax_task')) + + task_list = [] + cwd = os.getcwd() + + if self.reprod: + print('gamma line reproduce starts') + if 'init_data_path' not in self.parameter: + raise RuntimeError("please provide the initial data path to reproduce") + init_data_path = os.path.abspath(self.parameter['init_data_path']) + task_list = make_repro(init_data_path, self.init_from_suffix, + path_to_work, self.parameter.get('reprod_last_frame', True)) + os.chdir(cwd) + + else: + if refine: + print('gamma line refine starts') + task_list = make_refine(self.parameter['init_from_suffix'], + self.parameter['output_suffix'], + path_to_work) + os.chdir(cwd) + # record miller + init_from_path = re.sub(self.parameter['output_suffix'][::-1], + self.parameter['init_from_suffix'][::-1], + path_to_work[::-1], count=1)[::-1] + task_list_basename = list(map(os.path.basename, task_list)) + + for ii in task_list_basename: + init_from_task = os.path.join(init_from_path, ii) + output_task = os.path.join(path_to_work, ii) + os.chdir(output_task) + if os.path.isfile('miller.json'): + os.remove('miller.json') + if os.path.islink('miller.json'): + os.remove('miller.json') + os.symlink(os.path.relpath(os.path.join(init_from_task, 'miller.json')), 'miller.json') + os.chdir(cwd) + + else: + equi_contcar = os.path.join(path_to_equi, 'CONTCAR') + if not os.path.exists(equi_contcar): + raise RuntimeError("please do relaxation first") + print('we now only support gamma line calculation for BCC and FCC metals') + print('supported slip systems are planes/direction: 100/010, 110/111, 111/110, 111/112, 112/111, and 123/111') + ptypes = vasp.get_poscar_types(equi_contcar) + # read structure from relaxed CONTCAR + ss = Structure.from_file(equi_contcar) + # rewrite new CONTCAR with direct coords + os.chdir(path_to_equi) + ss.to('POSCAR', 'CONTCAR.direct') + # re-read new CONTCAR + ss = Structure.from_file('CONTCAR.direct') + relax_a = ss.lattice.a + relax_b = ss.lattice.b + relax_c = ss.lattice.c + # gen initial slab + slab = self.__gen_slab_ase(symbol=ptypes[0], + lat_param=[relax_a,relax_b,relax_c]) + # define displace vectors + disp_vector = (1/self.supercell_size[0], 0, 0) + # displace structure + all_slabs = self.__displace_slab(slab, disp_vector=disp_vector) + self.atom_num = len(all_slabs[0].sites) + + os.chdir(path_to_work) + if os.path.isfile('POSCAR'): + os.remove('POSCAR') + if os.path.islink('POSCAR'): + os.remove('POSCAR') + os.symlink(os.path.relpath(equi_contcar), 'POSCAR') + # task_poscar = os.path.join(output, 'POSCAR') + for ii in range(len(all_slabs)): + output_task = os.path.join(path_to_work, 'task.%06d' % ii) + os.makedirs(output_task, exist_ok=True) + os.chdir(output_task) + for jj in ['INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps']: + if os.path.exists(jj): + os.remove(jj) + task_list.append(output_task) + #print("# %03d generate " % ii, output_task) + print("# %03d generate " % ii, output_task, " \t %d atoms" % self.atom_num) + # make confs + all_slabs[ii].to('POSCAR', 'POSCAR.tmp') + vasp.regulate_poscar('POSCAR.tmp', 'POSCAR') + vasp.sort_poscar('POSCAR', 'POSCAR', ptypes) + # vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz) + # record miller + dumpfn(self.miller_index, 'miller.json') + os.chdir(cwd) + + return task_list + + @staticmethod + def centralize_slab(slab) -> None: + z_pos_list = list(set([site.position[2] for site in slab])) + z_pos_list.sort() + central_atoms = (z_pos_list[-1] - z_pos_list[0])/2 + central_cell = slab.cell[2][2]/2 + disp_length = central_cell - central_atoms + for site in slab: + site.position[2] += disp_length + + def return_direction(self): + miller_str = '' + direct_str = '' + for ii in range(len(self.miller_index)): + miller_str += str(self.miller_index[ii]) + for ii in range(len(self.displace_direction)): + direct_str += str(self.displace_direction[ii]) + search_key = miller_str + '/' + direct_str + # define specific cell vectors + dict_directions = { + '100/010': [(0,1,0), (0,0,1), (1,0,0)], + '110/111': [(-1,1,1), (1,-1,1), (1,1,0)], + '111/110': [(-1,1,0), (-1,-1,2), (1,1,1)], + '111/112': [(1,1,-2), (-1,1,0), (1,1,1)], + '112/111': [(-1,-1,1), (1,-1,0), (1,1,2)], + '123/111': [(-1,-1,1), (2,-1,0), (1,2,3)] + } + try: + directions = dict_directions[search_key] + except KeyError: + raise RuntimeError(f'Unsupported input combination of miller index and displacement direction: ' + f'{miller_str}:{direct_str}') + return directions + + def __gen_slab_ase(self, + symbol, lat_param): + if not self.lattice_type: + raise RuntimeError('Error! Please provide the input lattice type!') + elif self.lattice_type == 'bcc': + slab_ase = bcc(symbol=symbol, size=self.supercell_size, latticeconstant=lat_param[0], + directions=self.return_direction()) + elif self.lattice_type == 'fcc': + slab_ase = fcc(symbol=symbol, size=self.supercell_size, latticeconstant=lat_param[0], + directions=self.return_direction()) + elif self.lattice_type == 'hcp': + pass + else: + raise RuntimeError(f'unsupported lattice type: {self.lattice_type}') + self.centralize_slab(slab_ase) + if self.min_vacuum_size > 0: + slab_ase.center(vacuum=self.min_vacuum_size/2, axis=2) + slab_pymatgen = AseAtomsAdaptor.get_structure(slab_ase) + return slab_pymatgen + + # leave this function to later use + #def __gen_slab_pmg(self, + # pmg_struc): + # slabGen = SlabGenerator(pmg_struc, miller_index=self.miller_index, + # min_slab_size=self.supercell_size[2], + # min_vacuum_size=self.min_vacuum_size, + # center_slab=True, in_unit_planes=True, lll_reduce=False, + # primitive=True, max_normal_search=5) + # slab_pmg = slabGen.get_slab() + # slab_pmg.make_supercell(scaling_matrix=[self.supercell_size[0],self.supercell_size[1],1]) + # return slab_pmg + + def __displace_slab(self, + slab, disp_vector): + # return a list of displaced slab objects + all_slabs = [slab.copy()] + for ii in list(range(self.n_steps)): + frac_disp = 1 / self.n_steps + unit_vector = frac_disp * np.array(disp_vector) + # return list of atoms number to be displaced which above 0.5 z + disp_atoms_list = np.where(slab.frac_coords[:,2]>0.5)[0] + slab.translate_sites(indices=disp_atoms_list, vector=unit_vector, + frac_coords=True, to_unit_cell=True) + all_slabs.append(slab.copy()) + return all_slabs + + def __poscar_fix(self, poscar) -> None: + # add position fix condition of x and y in POSCAR + insert_pos = -self.atom_num + fix_dict = { + 'true': 'F', + 'false': 'T' + } + add_fix_str = ' ' + fix_dict[self.add_fix[0]] + \ + ' ' + fix_dict[self.add_fix[1]] + \ + ' ' + fix_dict[self.add_fix[2]] + '\n' + with open(poscar, 'r') as fin1: + contents = fin1.readlines() + contents.insert(insert_pos-1, 'Selective dynamics\n') + for ii in range(insert_pos, 0, 1): + contents[ii] = contents[ii].replace('\n', '') + contents[ii] += add_fix_str + with open(poscar, 'w') as fin2: + for ii in range(len(contents)): + fin2.write(contents[ii]) + + def __inLammpes_fix(self, inLammps) -> None: + # add position fix condition of x and y of in.lammps + fix_dict = { + 'true': '0', + 'false': 'NULL' + } + add_fix_str = 'fix 1 all setforce' + \ + ' ' + fix_dict[self.add_fix[0]] + \ + ' ' + fix_dict[self.add_fix[1]] + \ + ' ' + fix_dict[self.add_fix[2]] + '\n' + with open(inLammps, 'r') as fin1: + contents = fin1.readlines() + for ii in range(len(contents)): + upper = re.search("variable N equal count\(all\)", contents[ii]) + lower = re.search("min_style cg", contents[ii]) + if lower: + lower_id = ii + #print(lower_id) + elif upper: + upper_id = ii + #print(upper_id) + del contents[lower_id+1:upper_id-1] + contents.insert(lower_id+1, add_fix_str) + with open(inLammps, 'w') as fin2: + for ii in range(len(contents)): + fin2.write(contents[ii]) + + def post_process(self, + task_list): + if self.add_fix: + count = 0 + for ii in task_list: + count += 1 + inter = os.path.join(ii, 'inter.json') + poscar = os.path.join(ii, 'POSCAR') + calc_type = loadfn(inter)['type'] + if calc_type == 'vasp': + self.__poscar_fix(poscar) + else: + inLammps = os.path.join(ii, 'in.lammps') + if count == 1: + self.__inLammpes_fix(inLammps) + + + def task_type(self): + return self.parameter['type'] + + def task_param(self): + return self.parameter + + def _compute_lower(self, + output_file, + all_tasks, + all_res): + output_file = os.path.abspath(output_file) + res_data = {} + ptr_data = os.path.dirname(output_file) + '\n' + + if not self.reprod: + ptr_data += str(tuple(self.miller_index)) + ' plane along ' + str(self.displace_direction) + ptr_data += "No_task: \tDisplacement \tStacking_Fault_E(J/m^2) EpA(eV) slab_equi_EpA(eV)\n" + all_tasks.sort() + task_result_slab_equi = loadfn(os.path.join(all_tasks[0], 'result_task.json')) + for ii in all_tasks: + task_result = loadfn(os.path.join(ii, 'result_task.json')) + natoms = np.sum(task_result['atom_numbs']) + epa = task_result['energies'][-1] / natoms + equi_epa_slab = task_result_slab_equi['energies'][-1] / natoms + AA = np.linalg.norm(np.cross(task_result['cells'][0][0], task_result['cells'][0][1])) + + equi_path = os.path.abspath(os.path.join(os.path.dirname(output_file), '../relaxation/relax_task')) + equi_result = loadfn(os.path.join(equi_path, 'result.json')) + equi_epa = equi_result['energies'][-1] / np.sum(equi_result['atom_numbs']) + structure_dir = os.path.basename(ii) + + Cf = 1.60217657e-16 / 1e-20 * 0.001 + sfe = (task_result['energies'][-1] - task_result_slab_equi['energies'][-1]) / AA * Cf + + miller_index = loadfn(os.path.join(ii, 'miller.json')) + ptr_data += "%-25s %7.2f %7.3f %8.3f %8.3f\n" % ( + str(miller_index) + '-' + structure_dir + ':', int(ii[-4:])/self.n_steps, sfe, epa, equi_epa_slab) + res_data[int(ii[-4:])/self.n_steps] = [sfe, epa, equi_epa] + + + else: + if 'init_data_path' not in self.parameter: + raise RuntimeError("please provide the initial data path to reproduce") + init_data_path = os.path.abspath(self.parameter['init_data_path']) + res_data, ptr_data = post_repro(init_data_path, self.parameter['init_from_suffix'], + all_tasks, ptr_data, self.parameter.get('reprod_last_frame', True)) + + with open(output_file, 'w') as fp: + json.dump(res_data, fp, indent=4) + + return res_data, ptr_data diff --git a/dpgen/auto_test/Lammps.py b/dpgen/auto_test/Lammps.py index adc34eb93..d77b32716 100644 --- a/dpgen/auto_test/Lammps.py +++ b/dpgen/auto_test/Lammps.py @@ -120,8 +120,8 @@ def make_input_file(self, # dumpfn(task_param, os.path.join(output_dir, 'task.json'), indent=4) - etol = 1e-12 - ftol = 1e-6 + etol = 0 + ftol = 1e-10 maxiter = 5000 maxeval = 500000 B0 = 70 diff --git a/dpgen/auto_test/common_prop.py b/dpgen/auto_test/common_prop.py index 6bc7d9241..58074a95b 100644 --- a/dpgen/auto_test/common_prop.py +++ b/dpgen/auto_test/common_prop.py @@ -11,6 +11,7 @@ from dpgen.auto_test.Interstitial import Interstitial from dpgen.auto_test.Surface import Surface from dpgen.auto_test.Vacancy import Vacancy +from dpgen.auto_test.Gamma import Gamma from dpgen.auto_test.calculator import make_calculator from dpgen.dispatcher.Dispatcher import make_dispatcher from dpgen.dispatcher.Dispatcher import make_submission @@ -19,21 +20,23 @@ lammps_task_type = ['deepmd', 'meam', 'eam_fs', 'eam_alloy'] -def make_property_instance(paramters): +def make_property_instance(parameters): """ Make an instance of Property """ - prop_type = paramters['type'] + prop_type = parameters['type'] if prop_type == 'eos': - return EOS(paramters) + return EOS(parameters) elif prop_type == 'elastic': - return Elastic(paramters) + return Elastic(parameters) elif prop_type == 'vacancy': - return Vacancy(paramters) + return Vacancy(parameters) elif prop_type == 'interstitial': - return Interstitial(paramters) + return Interstitial(parameters) elif prop_type == 'surface': - return Surface(paramters) + return Surface(parameters) + elif prop_type == 'gamma': + return Gamma(parameters) else: raise RuntimeError(f'unknown property type {prop_type}') diff --git a/tests/auto_test/confs/hp-Mo/POSCAR b/tests/auto_test/confs/hp-Mo/POSCAR new file mode 100644 index 000000000..97240a378 --- /dev/null +++ b/tests/auto_test/confs/hp-Mo/POSCAR @@ -0,0 +1,13 @@ +Mo2 + 1.0000000000000000 + 3.1623672675177916 -0.0000000000000000 -0.0000000000000000 + -0.0000000000000000 3.1623672675177916 -0.0000000000000000 + 0.0000000000000000 0.0000000000000000 3.1623672675177916 + Mo + 2 +Direct + 0.0000000000000000 0.0000000000000000 0.0000000000000000 + 0.5000000000000000 0.5000000000000000 0.5000000000000000 + + 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 diff --git a/tests/auto_test/equi/vasp/CONTCAR_Mo_bcc b/tests/auto_test/equi/vasp/CONTCAR_Mo_bcc new file mode 100644 index 000000000..2523bde84 --- /dev/null +++ b/tests/auto_test/equi/vasp/CONTCAR_Mo_bcc @@ -0,0 +1,10 @@ +Mo2 +1.0 +3.1617699325125632e+00 0.0000000000000000e+00 0.0000000000000000e+00 +-2.9607253805968378e-17 3.1617699325125632e+00 0.0000000000000000e+00 +-6.1517551630255350e-18 -4.3742379676789617e-17 3.1617699325125632e+00 +Mo +2 +Cartesian + 0.0000000000 0.0000000000 0.0000000000 + 1.5808849663 1.5808849663 1.5808849663 diff --git a/tests/auto_test/output/gamma_00/POSCAR b/tests/auto_test/output/gamma_00/POSCAR new file mode 120000 index 000000000..75eec9b68 --- /dev/null +++ b/tests/auto_test/output/gamma_00/POSCAR @@ -0,0 +1 @@ +../relaxation/relax_task/CONTCAR \ No newline at end of file diff --git a/tests/auto_test/output/gamma_00/in.lammps b/tests/auto_test/output/gamma_00/in.lammps new file mode 100644 index 000000000..d7b39b0a5 --- /dev/null +++ b/tests/auto_test/output/gamma_00/in.lammps @@ -0,0 +1,38 @@ +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +box tilt large +read_data conf.lmp +mass 1 95.940 +neigh_modify every 1 delay 0 check no +pair_style deepmd frozen_model.pb +pair_coeff * * +compute mype all pe +thermo 100 +thermo_style custom step pe pxx pyy pzz pxy pxz pyz lx ly lz vol c_mype +dump 1 all custom 100 dump.relax id type xs ys zs fx fy fz +min_style cg +fix 1 all setforce 0 0 NULL +minimize 0.000000e+00 1.000000e-10 5000 500000 +variable N equal count(all) +variable V equal vol +variable E equal "c_mype" +variable tmplx equal lx +variable tmply equal ly +variable Pxx equal pxx +variable Pyy equal pyy +variable Pzz equal pzz +variable Pxy equal pxy +variable Pxz equal pxz +variable Pyz equal pyz +variable Epa equal ${E}/${N} +variable Vpa equal ${V}/${N} +variable AA equal (${tmplx}*${tmply}) +print "All done" +print "Total number of atoms = ${N}" +print "Final energy per atoms = ${Epa}" +print "Final volume per atoms = ${Vpa}" +print "Final Base area = ${AA}" +print "Final Stress (xx yy zz xy xz yz) = ${Pxx} ${Pyy} ${Pzz} ${Pxy} ${Pxz} ${Pyz}" diff --git a/tests/auto_test/output/gamma_00/task.000000/CONTCAR b/tests/auto_test/output/gamma_00/task.000000/CONTCAR new file mode 100644 index 000000000..1c13e161c --- /dev/null +++ b/tests/auto_test/output/gamma_00/task.000000/CONTCAR @@ -0,0 +1,508 @@ +Mo500 +1.0 +1.3677680000000001e+01 0.0000000000000000e+00 0.0000000000000000e+00 +-4.5592269999999999e+00 1.2895441000000000e+01 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 6.2437561000000002e+01 +Mo +500 +Cartesian + 0.0000000000 0.0000000000 10.1387360303 + 0.9118453000 1.2895441000 12.2416955223 + 2.7355360000 0.0000000000 10.1387360303 + 3.6473813000 1.2895441000 12.2416955223 + 5.4710720000 0.0000000000 10.1387360303 + 6.3829173000 1.2895441000 12.2416955223 + 8.2066080000 0.0000000000 10.1387360303 + 9.1184533000 1.2895441000 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hcp + +import dpgen.auto_test.lib.vasp as vasp +from dpgen import dlog +from dpgen.auto_test.Property import Property +from dpgen.auto_test.refine import make_refine +from dpgen.auto_test.reproduce import make_repro +from dpgen.auto_test.reproduce import post_repro + +sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) +__package__ = 'auto_test' + +from .context import make_kspacing_kpoints +from .context import setUpModule + +from dpgen.auto_test.Gamma import Gamma + +class TestGamma(unittest.TestCase): + + def setUp(self): + _jdata = { + "structures": ["confs/std-fcc"], + "interaction": { + "type": "vasp", + "incar": "vasp_input/INCAR_Mo", + "potcar_prefix": "vasp_input", + "potcars": {"Mo": "POTCAR_Mo"} + }, + "properties": [ + { + "type": "gamma", + "lattice_type": "fcc", + "miller_index": [1, 1, 1], + "displace_direction": [1, 1, 0], + "supercell_size": [1, 1, 10], + "min_vacuum_size": 10, + "add_fix": ["true", "true", "false"], + "n_steps": 20 + } + ] + } + + self.equi_path = 'confs/hp-Mo/relaxation/relax_task' + self.source_path = 'equi/vasp' + self.target_path = 'confs/hp-Mo/gamma_00' + self.res_data = 'output/gamma_00/result.json' + self.ptr_data = 'output/gamma_00/result.out' + + if not os.path.exists(self.equi_path): + os.makedirs(self.equi_path) + if not os.path.exists(self.target_path): + os.makedirs(self.target_path) + + self.confs = _jdata["structures"] + self.inter_param = _jdata["interaction"] + self.prop_param = _jdata['properties'] + + self.gamma = Gamma(_jdata['properties'][0]) + + def tearDown(self): + if os.path.exists(self.equi_path): + shutil.rmtree(self.equi_path) + if os.path.exists(self.target_path): + shutil.rmtree(self.target_path) + if os.path.exists(self.res_data): + os.remove(self.res_data) + if os.path.exists(self.ptr_data): + os.remove(self.ptr_data) + + def test_task_type(self): + self.assertEqual('gamma', self.gamma.task_type()) + + def test_task_param(self): + self.assertEqual(self.prop_param[0], self.gamma.task_param()) + + def test_make_confs_bcc(self): + if not os.path.exists(os.path.join(self.equi_path, 'CONTCAR')): + with self.assertRaises(RuntimeError): + self.gamma.make_confs(self.target_path, self.equi_path) + shutil.copy(os.path.join(self.source_path, 'CONTCAR_Mo_bcc'), os.path.join(self.equi_path, 'CONTCAR')) + task_list = self.gamma.make_confs(self.target_path, self.equi_path) + dfm_dirs = glob.glob(os.path.join(self.target_path, 'task.*')) + self.assertEqual(len(dfm_dirs), self.gamma.n_steps+1) + + incar0 = Incar.from_file(os.path.join('vasp_input', 'INCAR.rlx')) + incar0['ISIF'] = 4 + + self.assertEqual(os.path.realpath(os.path.join(self.equi_path, 'CONTCAR')), + os.path.realpath(os.path.join(self.target_path, 'POSCAR'))) + ref_st = Structure.from_file(os.path.join(self.target_path, 'POSCAR')) + dfm_dirs.sort() + for ii in dfm_dirs: + st_file = os.path.join(ii, 'POSCAR') + self.assertTrue(os.path.isfile(st_file)) + st0 = Structure.from_file(st_file) + st1_file = os.path.join(ii, 'POSCAR.tmp') + self.assertTrue(os.path.isfile(st1_file)) + st1 = Structure.from_file(st1_file) + with open(st1_file, mode='r') as f: + z_coord_str = f.readlines()[-1].split()[-2] + z_coord = float(z_coord_str) + self.assertTrue(z_coord <= 1) + + def test_compute_lower(self): + cwd = os.getcwd() + output_file = os.path.join(cwd, 'output/gamma_00/result.json') + all_tasks = glob.glob('output/gamma_00/task.*') + all_tasks.sort() + all_res = [os.path.join(task, 'result_task.json') for task in all_tasks] + + self.gamma._compute_lower(output_file, + all_tasks, + all_res) + + self.assertTrue(os.path.isfile(self.res_data)) + diff --git a/tests/auto_test/vasp_input/INCAR_Mo b/tests/auto_test/vasp_input/INCAR_Mo new file mode 100644 index 000000000..3750b7794 --- /dev/null +++ b/tests/auto_test/vasp_input/INCAR_Mo @@ -0,0 +1,33 @@ +#Parameters +SYSTEM = Mo_hcp +PREC = Accurate +ISTART = 0 +ICHARG = 2 +#Electronic Relaxation +ENCUT = 800 # test +NELM = 100 +NELMIN = 6 +NELMDL = -5 +EDIFF = 1e-06 # test +LREAL = False +ALGO = Normal # or normal +#Ionic relaxation +IBRION = 2 +#POTIM = 0.3 +ISIF = 3 +EDIFFG = -0.01 # test +#ISYM = 0 +NSW = 100 +ISMEAR = 1 +SIGMA = 0.1 # test +# Write flags +LWAVE = False +LCHARG = False +#parallel related +#KPAR = 16 +NPAR = 4 +#KPAR = 1 +KSPACING = 0.1 # test +KGAMMA = False + +PSTRESS = 0.0 diff --git a/tests/auto_test/vasp_input/POTCAR_Mo b/tests/auto_test/vasp_input/POTCAR_Mo new file mode 100644 index 000000000..70dfaf57c --- /dev/null +++ b/tests/auto_test/vasp_input/POTCAR_Mo @@ -0,0 +1 @@ +2731df97e41766cc617548c5a8267718fdef1f509ac6bafa01e745abea2bdfaa