diff --git a/.gitignore b/.gitignore index 22da09a0c..76ac02d1d 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,4 @@ build dist dpdata.egg-info _version.py +!tests/cp2k/aimd/cp2k.log diff --git a/README.md b/README.md index 77d0dcbf8..ae0418030 100644 --- a/README.md +++ b/README.md @@ -99,9 +99,10 @@ xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/') | deepmd | npy | True | True | LabeledSystem | 'deepmd/npy' | | gaussian| log | False | True | LabeledSystem | 'gaussian/log'| | gaussian| log | True | True | LabeledSystem | 'gaussian/md' | -| siesta| output | False | True | LabeledSystem | 'siesta/output'| -| siesta| aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' | +| siesta | output | False | True | LabeledSystem | 'siesta/output'| +| siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' | | cp2k | output | False | True | LabeledSystem | 'cp2k/output' | +| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' | | QE | log | False | True | LabeledSystem | 'qe/pw/scf' | | QE | log | True | False | System | 'qe/cp/traj' | | QE | log | True | True | LabeledSystem | 'qe/cp/traj' | @@ -152,3 +153,20 @@ Frame selection can be implemented by dpdata.LabeledSystem('OUTCAR').sub_system([0,-1]).to_deepmd_raw('dpmd_raw') ``` by which only the first and last frames are dumped to `dpmd_raw`. + +## replicate +dpdata will create a super cell of the current atom configuration. +```python +dpdata.System('./POSCAR').replicate((1,2,3,) ) +``` +tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction. + +## perturb +By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere). +```python +perturbed_system = dpdata.System('./POSCAR').perturb(pert_num=3, + cell_pert_fraction=0.05, + atom_pert_distance=0.6, + atom_pert_style='normal') +print(perturbed_system.data) +``` diff --git a/dpdata/cp2k/__init__.py b/dpdata/cp2k/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/cp2k/cell.py b/dpdata/cp2k/cell.py new file mode 100644 index 000000000..017986ec1 --- /dev/null +++ b/dpdata/cp2k/cell.py @@ -0,0 +1,61 @@ + +#%% +import numpy as np +from collections import OrderedDict +import re + +def cell_to_low_triangle(A,B,C,alpha,beta,gamma): + """ + Convert cell to low triangle matrix. + + Parameters + ---------- + A : float + cell length A + B : float + cell length B + C : float + cell length C + alpha : float + radian. The angle between vector B and vector C. + beta : float + radian. The angle between vector A and vector C. + gamma : float + radian. The angle between vector B and vector C. + + Returns + ------- + cell : list + The cell matrix used by dpdata in low triangle form. + """ + if not np.pi*5/180 0.2: + raise RuntimeError("A=={}, must be greater than 0.2".format(A)) + if not B > 0.2: + raise RuntimeError("B=={}, must be greater than 0.2".format(B)) + if not C > 0.2: + raise RuntimeError("C=={}, must be greater than 0.2".format(C)) + + lx = A + xy = B * np.cos(gamma) + xz = C * np.cos(beta) + ly = B* np.sin(gamma) + if not ly > 0.1: + raise RuntimeError("ly:=B* np.sin(gamma)=={}, must be greater than 0.1",format(ly)) + yz = (B*C*np.cos(alpha)-xy*xz)/ly + if not C**2-xz**2-yz**2 > 0.01: + raise RuntimeError("lz^2:=C**2-xz**2-yz**2=={}, must be greater than 0.01",format(C**2-xz**2-yz**2)) + lz = np.sqrt(C**2-xz**2-yz**2) + cell = np.asarray([[lx, 0 , 0], + [xy, ly, 0 ], + [xz, yz, lz]]).astype('float32') + return cell + diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index ebd56b0ec..f9b96eb42 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -1,11 +1,217 @@ +#%% import numpy as np +import re +from collections import OrderedDict +from .cell import cell_to_low_triangle +#%% +AU_TO_ANG = 5.29177208590000E-01 +AU_TO_EV = 2.72113838565563E+01 +AU_TO_EV_EVERY_ANG = AU_TO_EV/AU_TO_ANG +delimiter_patterns=[] +delimiter_p1 = re.compile(r'^ \* GO CP2K GO! \*+') +delimiter_p2 = re.compile(r'^ \*+') +delimiter_patterns.append(delimiter_p1) +delimiter_patterns.append(delimiter_p2) +avail_patterns = [] + +avail_patterns.append(re.compile(r'^ INITIAL POTENTIAL ENERGY')) +avail_patterns.append(re.compile(r'^ ENSEMBLE TYPE')) + +class Cp2kSystems(object): + """ + deal with cp2k outputfile + """ + def __init__(self, log_file_name, xyz_file_name): + self.log_file_object = open(log_file_name, 'r') + self.xyz_file_object = open(xyz_file_name, 'r') + self.log_block_generator = self.get_log_block_generator() + self.xyz_block_generator = self.get_xyz_block_generator() + self.cell=None + def __del__(self): + self.log_file_object.close() + self.xyz_file_object.close() + def __iter__(self): + return self + def __next__(self): + info_dict = {} + log_info_dict = self.handle_single_log_frame(next(self.log_block_generator)) + xyz_info_dict = self.handle_single_xyz_frame(next(self.xyz_block_generator)) + eq1 = [v1==v2 for v1,v2 in zip(log_info_dict['atom_numbs'], xyz_info_dict['atom_numbs'])] + eq2 = [v1==v2 for v1,v2 in zip(log_info_dict['atom_names'], xyz_info_dict['atom_names'])] + eq3 = [v1==v2 for v1,v2 in zip(log_info_dict['atom_types'], xyz_info_dict['atom_types'])] + assert all(eq1), (log_info_dict,xyz_info_dict,'There may be errors in the file') + assert all(eq2), (log_info_dict,xyz_info_dict,'There may be errors in the file') + assert all(eq3), (log_info_dict,xyz_info_dict,'There may be errors in the file') + assert log_info_dict['energies']==xyz_info_dict['energies'], (log_info_dict['energies'],xyz_info_dict['energies'],'There may be errors in the file') + info_dict.update(log_info_dict) + info_dict.update(xyz_info_dict) + return info_dict + + def get_log_block_generator(self): + lines = [] + delimiter_flag = False + while True: + line = self.log_file_object.readline() + if line: + lines.append(line) + if any(p.match(line) for p in delimiter_patterns): + if delimiter_flag is True: + yield lines + lines = [] + delimiter_flag = False + else: + line = self.log_file_object.readline() + lines.append(line) + if any(p.match(line) for p in avail_patterns): + delimiter_flag = True + else: + break + if delimiter_flag is True: + raise RuntimeError('This file lacks some content, please check') + + def get_xyz_block_generator(self): + p3 = re.compile(r'^\s*(\d+)\s*') + while True: + line = self.xyz_file_object.readline() + if not line: + break + if p3.match(line): + atom_num = int(p3.match(line).group(1)) + lines = [] + lines.append(line) + for ii in range(atom_num+1): + lines.append(self.xyz_file_object.readline()) + if not lines[-1]: + raise RuntimeError("this xyz file may lack of lines, should be {};lines:{}".format(atom_num+2, lines)) + yield lines + + def handle_single_log_frame(self, lines): + info_dict={} + energy_pattern_1 = re.compile(r' INITIAL POTENTIAL ENERGY\[hartree\]\s+=\s+(?P\S+)') + # CONSERVED QUANTITY [hartree] = -0.279168013085E+04 + energy_pattern_2 = re.compile(r' POTENTIAL ENERGY\[hartree\]\s+=\s+(?P\S+)') + energy=None + cell_length_pattern = re.compile(r' INITIAL CELL LNTHS\[bohr\]\s+=\s+(?P\S+)\s+(?P\S+)\s+(?P\S+)') + cell_angle_pattern = re.compile(r' INITIAL CELL ANGLS\[deg\]\s+=\s+(?P\S+)\s+(?P\S+)\s+(?P\S+)') + cell_A, cell_B, cell_C = (0,0,0,) + cell_alpha, cell_beta, cell_gamma=(0,0,0,) + force_start_pattern = re.compile(r' ATOMIC FORCES in') + force_flag=False + force_end_pattern = re.compile(r' SUM OF ATOMIC FORCES') + force_lines= [] + cell_flag=0 + for line in lines: + if force_start_pattern.match(line): + force_flag=True + if force_end_pattern.match(line): + assert force_flag is True, (force_flag,'there may be errors in this file ') + force_flag=False + if force_flag is True: + force_lines.append(line) + if energy_pattern_1.match(line): + energy = float(energy_pattern_1.match(line).groupdict()['number']) * AU_TO_EV + if energy_pattern_2.match(line): + energy = float(energy_pattern_2.match(line).groupdict()['number']) * AU_TO_EV + if cell_length_pattern.match(line): + cell_A = float(cell_length_pattern.match(line).groupdict()['A']) * AU_TO_ANG + cell_B = float(cell_length_pattern.match(line).groupdict()['B']) * AU_TO_ANG + cell_C = float(cell_length_pattern.match(line).groupdict()['C']) * AU_TO_ANG + cell_flag+=1 + if cell_angle_pattern.match(line): + cell_alpha = np.deg2rad(float(cell_angle_pattern.match(line).groupdict()['alpha'])) + cell_beta = np.deg2rad(float(cell_angle_pattern.match(line).groupdict()['beta'])) + cell_gamma = np.deg2rad(float(cell_angle_pattern.match(line).groupdict()['gamma'])) + cell_flag+=1 + if cell_flag == 2: + self.cell = cell_to_low_triangle(cell_A,cell_B,cell_C, + cell_alpha,cell_beta,cell_gamma) + # lx = cell_A + # xy = cell_B * np.cos(cell_gamma) + # xz = cell_C * np.cos(cell_beta) + # ly = cell_B* np.sin(cell_gamma) + # yz = (cell_B*cell_C*np.cos(cell_alpha)-xy*xz)/ly + # lz = np.sqrt(cell_C**2-xz**2-yz**2) + # self.cell = [[lx, 0 , 0], + # [xy, ly, 0 ], + # [xz, yz, lz]] + + element_index = -1 + element_dict = OrderedDict() + atom_types_list = [] + forces_list = [] + for line in force_lines[3:]: + line_list = line.split() + if element_dict.get(line_list[2]): + element_dict[line_list[2]][1]+=1 + else: + element_index +=1 + element_dict[line_list[2]]=[element_index,1] + atom_types_list.append(element_dict[line_list[2]][0]) + forces_list.append([float(line_list[3])*AU_TO_EV_EVERY_ANG, + float(line_list[4])*AU_TO_EV_EVERY_ANG, + float(line_list[5])*AU_TO_EV_EVERY_ANG]) + + atom_names=list(element_dict.keys()) + atom_numbs=[] + for ii in atom_names: + atom_numbs.append(element_dict[ii][1]) + info_dict['atom_names'] = atom_names + info_dict['atom_numbs'] = atom_numbs + info_dict['atom_types'] = np.asarray(atom_types_list) + info_dict['cells'] = np.asarray([self.cell]).astype('float32') + info_dict['energies'] = np.asarray([energy]).astype('float32') + info_dict['forces'] = np.asarray([forces_list]).astype('float32') + return info_dict + + def handle_single_xyz_frame(self, lines): + info_dict = {} + atom_num = int(lines[0].strip('\n').strip()) + if len(lines) != atom_num + 2: + raise RuntimeError("format error, atom_num=={}, {}!=atom_num+2".format(atom_num, len(lines))) + data_format_line = lines[1].strip('\n').strip()+str(' ') + prop_pattern = re.compile(r'(?P\w+)\s*=\s*(?P.*?)[, ]') + prop_dict = dict(prop_pattern.findall(data_format_line)) + + energy=0 + if prop_dict.get('E'): + energy = float(prop_dict.get('E')) * AU_TO_EV + # info_dict['energies'] = np.array([prop_dict['E']]).astype('float32') + + element_index = -1 + element_dict = OrderedDict() + atom_types_list = [] + coords_list = [] + for line in lines[2:]: + line_list = line.split() + if element_dict.get(line_list[0]): + element_dict[line_list[0]][1]+=1 + else: + element_index +=1 + element_dict[line_list[0]]=[element_index,1] + atom_types_list.append(element_dict[line_list[0]][0]) + coords_list.append([float(line_list[1])*AU_TO_ANG, + float(line_list[2])*AU_TO_ANG, + float(line_list[3])*AU_TO_ANG]) + atom_names=list(element_dict.keys()) + atom_numbs=[] + for ii in atom_names: + atom_numbs.append(element_dict[ii][1]) + info_dict['atom_names'] = atom_names + info_dict['atom_numbs'] = atom_numbs + info_dict['atom_types'] = np.asarray(atom_types_list) + info_dict['coords'] = np.asarray([coords_list]).astype('float32') + info_dict['energies'] = np.array([energy]).astype('float32') + info_dict['orig']=[0,0,0] + return info_dict + +#%% def get_frames (fname) : coord_flag = False force_flag = False - eV = 2.72113838565563E+01 - angstrom = 5.29177208590000E-01 + eV = 2.72113838565563E+01 # hatree to eV + angstrom = 5.29177208590000E-01 # Bohrto Angstrom fp = open(fname) atom_symbol_list = [] cell = [] @@ -74,3 +280,6 @@ def get_frames (fname) : return list(atom_names), atom_numbs, atom_types, cell, coord, energy, force + + +# %% diff --git a/dpdata/deepmd/__init__.py b/dpdata/deepmd/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py index 326e7087e..5f52c1a0f 100644 --- a/dpdata/deepmd/comp.py +++ b/dpdata/deepmd/comp.py @@ -48,6 +48,8 @@ def to_system_data(folder, data['forces'] = np.concatenate(all_forces, axis = 0) if len(all_virs) > 0: data['virials'] = np.concatenate(all_virs, axis = 0) + if os.path.isfile(os.path.join(folder, "nopbc")): + data['nopbc'] = True return data @@ -101,5 +103,10 @@ def dump(folder, np.save(os.path.join(set_folder, 'virial'), virials[set_stt:set_end]) if 'atom_pref' in data: np.save(os.path.join(set_folder, "atom_pref"), atom_pref[set_stt:set_end]) - + try: + os.remove(os.path.join(folder, "nopbc")) + except OSError: + pass + if data.get("nopbc", False): + os.mknod(os.path.join(folder, "nopbc")) diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py index 500c4bad9..039b3b787 100644 --- a/dpdata/deepmd/raw.py +++ b/dpdata/deepmd/raw.py @@ -49,6 +49,8 @@ def to_system_data(folder, type_map = None, labels = True) : if os.path.exists(os.path.join(folder, 'virial.raw')) : data['virials'] = np.loadtxt(os.path.join(folder, 'virial.raw')) data['virials'] = np.reshape(data['virials'], [nframes, 3, 3]) + if os.path.isfile(os.path.join(folder, "nopbc")): + data['nopbc'] = True return data else : raise RuntimeError('not dir ' + folder) @@ -67,5 +69,10 @@ def dump (folder, data) : np.savetxt(os.path.join(folder, 'force.raw'), np.reshape(data['forces'], [nframes, -1])) if 'virials' in data : np.savetxt(os.path.join(folder, 'virial.raw'), np.reshape(data['virials'], [nframes, 9])) - + try: + os.remove(os.path.join(folder, "nopbc")) + except OSError: + pass + if data.get("nopbc", False): + os.mknod(os.path.join(folder, "nopbc")) diff --git a/dpdata/gaussian/__init__.py b/dpdata/gaussian/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/gaussian/log.py b/dpdata/gaussian/log.py index 8d6c96a4e..ff28e09e3 100644 --- a/dpdata/gaussian/log.py +++ b/dpdata/gaussian/log.py @@ -69,4 +69,5 @@ def to_system_data(file_name, md=False): data['coords'] = np.array(coords_t) data['orig'] = np.array([0, 0, 0]) data['cells'] = np.array([[[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]] for _ in energy_t]) + data['nopbc'] = True return data diff --git a/dpdata/lammps/__init__.py b/dpdata/lammps/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/md/__init__.py b/dpdata/md/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/md/water.py b/dpdata/md/water.py index afc171a3d..8c38a108a 100644 --- a/dpdata/md/water.py +++ b/dpdata/md/water.py @@ -1,12 +1,76 @@ import numpy as np from .pbc import posi_diff -def compute_bonds(box, - posis, - atype, - oh_sel = [0,1], - max_roh = 1.3, - uniq_hbond = True): +def compute_bonds (box, + posis, + atype, + oh_sel = [0,1], + max_roh = 1.3, + uniq_hbond = True): + try : + import ase + import ase.neighborlist + # nlist implemented by ase + return compute_bonds_ase(box, posis, atype, oh_sel, max_roh, uniq_hbond) + except ImportError: + # nlist naivly implemented , scales as O(N^2) + return compute_bonds_naive(box, posis, atype, oh_sel, max_roh, uniq_hbond) + + +def compute_bonds_ase(box, + posis, + atype, + oh_sel = [0,1], + max_roh = 1.3, + uniq_hbond = True): + natoms = len(posis) + from ase import Atoms + import ase.neighborlist + atoms = Atoms(positions=posis, cell=box, pbc=[1,1,1]) + nlist = ase.neighborlist.NeighborList(max_roh, self_interaction=False, bothways=True, primitive=ase.neighborlist.NewPrimitiveNeighborList) + nlist.update(atoms) + bonds = [] + o_type = oh_sel[0] + h_type = oh_sel[1] + for ii in range(natoms) : + bonds.append([]) + for ii in range(natoms) : + if atype[ii] == o_type : + nn, ss = nlist.get_neighbors(ii) + for jj in nn: + if atype[jj] == h_type : + dr = posi_diff(box, posis[ii], posis[jj]) + if np.linalg.norm(dr) < max_roh : + bonds[ii].append(jj) + bonds[jj].append(ii) + if uniq_hbond : + for jj in range(natoms) : + if atype[jj] == h_type : + if len(bonds[jj]) > 1 : + orig_bonds = bonds[jj] + min_bd = 1e10 + min_idx = -1 + for ii in bonds[jj] : + dr = posi_diff(box, posis[ii], posis[jj]) + drr = np.linalg.norm(dr) + # print(ii,jj, posis[ii], posis[jj], drr) + if drr < min_bd : + min_idx = ii + min_bd = drr + bonds[jj] = [min_idx] + orig_bonds.remove(min_idx) + # print(min_idx, orig_bonds, bonds[jj]) + for ii in orig_bonds : + bonds[ii].remove(jj) + return bonds + + +def compute_bonds_naive(box, + posis, + atype, + oh_sel = [0,1], + max_roh = 1.3, + uniq_hbond = True): natoms = len(posis) bonds = [] o_type = oh_sel[0] diff --git a/dpdata/qe/__init__.py b/dpdata/qe/__init__.py new file mode 100644 index 000000000..d3f5a12fa --- /dev/null +++ b/dpdata/qe/__init__.py @@ -0,0 +1 @@ + diff --git a/dpdata/system.py b/dpdata/system.py index aaba652b7..c129b8778 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -16,6 +16,7 @@ import dpdata.md.pbc import dpdata.gaussian.log import dpdata.cp2k.output +from dpdata.cp2k.output import Cp2kSystems from copy import deepcopy from monty.json import MSONable from monty.serialization import loadfn,dumpfn @@ -284,6 +285,7 @@ def sub_system(self, f_idx) : tmp.data[ii] = self.data[ii] tmp.data['cells'] = self.data['cells'][f_idx].reshape(-1, 3, 3) tmp.data['coords'] = self.data['coords'][f_idx].reshape(-1, self.data['coords'].shape[1], 3) + tmp.data['nopbc'] = self.nopbc return tmp @@ -319,6 +321,9 @@ def append(self, system) : assert(all(eq)) for ii in ['coords', 'cells'] : self.data[ii] = np.concatenate((self.data[ii], system[ii]), axis = 0) + if self.nopbc and not system.nopbc: + # appended system uses PBC, cancel nopbc + self.data['nopbc'] = False return True def sort_atom_names(self, type_map=None): @@ -416,6 +421,43 @@ def from_lammps_lmp (self, file_name, type_map = None) : self.data = dpdata.lammps.lmp.to_system_data(lines, type_map) self._shift_orig_zero() + def to_pymatgen_structure(self): + ''' + convert System to Pymatgen Structure obj + + ''' + structures=[] + try: + from pymatgen import Structure + except: + raise ImportError('No module pymatgen.Structure') + + for system in self.to_list(): + species=[] + for name,numb in zip(system.data['atom_names'],system.data['atom_numbs']): + species.extend([name]*numb) + structure=Structure(system.data['cells'][0],species,system.data['coords'][0],coords_are_cartesian=True) + structures.append(structure) + return structures + + def to_ase_structure(self): + ''' + convert System to ASE Atom obj + + ''' + structures=[] + try: + from ase import Atoms + except: + raise ImportError('No module ase.Atoms') + + for system in self.to_list(): + species=[] + for name,numb in zip(system.data['atom_names'],system.data['atom_numbs']): + species.extend([name]*numb) + structure=Atoms(symbols=species,positions=system.data['coords'][0],pbc=True,cell=system.data['cells'][0]) + structures.append(structure) + return structures def to_lammps_lmp(self, file_name, frame_idx = 0) : """ @@ -450,7 +492,19 @@ def from_vasp_poscar(self, file_name) : self.data = dpdata.vasp.poscar.to_system_data(lines) self.rot_lower_triangular() - + def to_vasp_string(self, frame_idx=0): + """ + Dump the system in vasp POSCAR format string + + Parameters + ---------- + frame_idx : int + The index of the frame to dump + """ + assert(frame_idx < len(self.data['coords'])) + w_str = dpdata.vasp.poscar.from_system_data(self.data, frame_idx) + return w_str + def to_vasp_poscar(self, file_name, frame_idx = 0) : """ Dump the system in vasp POSCAR format @@ -462,8 +516,7 @@ def to_vasp_poscar(self, file_name, frame_idx = 0) : frame_idx : int The index of the frame to dump """ - assert(frame_idx < len(self.data['coords'])) - w_str = dpdata.vasp.poscar.from_system_data(self.data, frame_idx) + w_str=self.to_vasp_string( frame_idx= frame_idx ) with open(file_name, 'w') as fp: fp.write(w_str) @@ -579,6 +632,148 @@ def add_atom_names(self, atom_names): self.data['atom_names'].extend(atom_names) self.data['atom_numbs'].extend([0 for _ in atom_names]) + def replicate(self, ncopy): + """ + Replicate the each frame in the system in 3 dimensions. + Each frame in the system will become a supercell. + + Parameters + ---------- + ncopy : + list: [4,2,3] + or tuple: (4,2,3,) + make `ncopy[0]` copys in x dimensions, + make `ncopy[1]` copys in y dimensions, + make `ncopy[2]` copys in z dimensions. + + Returns + ------- + tmp : System + The system after replication. + """ + if len(ncopy) !=3: + raise RuntimeError('ncopy must be a list or tuple with 3 int') + for ii in ncopy: + if type(ii) is not int: + raise RuntimeError('ncopy must be a list or tuple must with 3 int') + + tmp = System() + nframes = self.get_nframes() + data = self.data + tmp.data['atom_names'] = list(np.copy(data['atom_names'])) + tmp.data['atom_numbs'] = list(np.array(np.copy(data['atom_numbs'])) * np.prod(ncopy)) + tmp.data['atom_types'] = np.sort(np.tile(np.copy(data['atom_types']),np.prod(ncopy))) + tmp.data['cells'] = np.copy(data['cells']) + for ii in range(3): + tmp.data['cells'][:,ii,:] *= ncopy[ii] + tmp.data['coords'] = np.tile(np.copy(data['coords']),tuple(ncopy)+(1,1,1)) + + for xx in range(ncopy[0]): + for yy in range(ncopy[1]): + for zz in range(ncopy[2]): + tmp.data['coords'][xx,yy,zz,:,:,:] += xx * np.reshape(data['cells'][:,0,:], [-1,1,3])\ + + yy * np.reshape(data['cells'][:,1,:], [-1,1,3])\ + + zz * np.reshape(data['cells'][:,2,:], [-1,1,3]) + tmp.data['coords'] = np.reshape(np.transpose(tmp.data['coords'], [3,4,0,1,2,5]), (nframes, -1 , 3)) + return tmp + + def perturb(self, + pert_num, + cell_pert_fraction, + atom_pert_distance, + atom_pert_style='normal'): + """ + Perturb each frame in the system randomly. + The cell will be deformed randomly, and atoms will be displaced by a random distance in random direction. + + Parameters + ---------- + pert_num : int + Each frame in the system will make `pert_num` copies, + and all the copies will be perturbed. + That means the system to be returned will contain `pert_num` * frame_num of the input system. + cell_pert_fraction : float + A fraction determines how much (relatively) will cell deform. + The cell of each frame is deformed by a symmetric matrix perturbed from identity. + The perturbation to the diagonal part is subject to a uniform distribution in [-cell_pert_fraction, cell_pert_fraction), + and the perturbation to the off-diagonal part is subject to a uniform distribution in [-0.5*cell_pert_fraction, 0.5*cell_pert_fraction). + atom_pert_distance: float + unit: Angstrom. A distance determines how far atoms will move. + Atoms will move about `atom_pert_distance` in random direction. + The distribution of the distance atoms move is determined by atom_pert_style + atom_pert_style : str + Determines the distribution of the distance atoms move is subject to. + Avaliable options are + - `'normal'`: the `distance` will be object to `chi-square distribution with 3 degrees of freedom` after normalization. + The mean value of the distance is `atom_pert_fraction*side_length` + - `'uniform'`: will generate uniformly random points in a 3D-balls with radius as `atom_pert_distance`. + These points are treated as vector used by atoms to move. + Obviously, the max length of the distance atoms move is `atom_pert_distance`. + - `'const'`: The distance atoms move will be a constant `atom_pert_distance`. + + Returns + ------- + perturbed_system : System + The perturbed_system. It contains `pert_num` * frame_num of the input system frames. + """ + perturbed_system = System() + nframes = self.get_nframes() + for ii in range(nframes): + for jj in range(pert_num): + tmp_system = self[ii].copy() + cell_perturb_matrix = get_cell_perturb_matrix(cell_pert_fraction) + tmp_system.data['cells'][0] = np.matmul(tmp_system.data['cells'][0],cell_perturb_matrix) + tmp_system.data['coords'][0] = np.matmul(tmp_system.data['coords'][0],cell_perturb_matrix) + for kk in range(len(tmp_system.data['coords'][0])): + atom_perturb_vector = get_atom_perturb_vector(atom_pert_distance, atom_pert_style) + tmp_system.data['coords'][0][kk] += atom_perturb_vector + tmp_system.rot_lower_triangular() + perturbed_system.append(tmp_system) + return perturbed_system + + @property + def nopbc(self): + if self.data.get("nopbc", False): + return True + return False + +def get_cell_perturb_matrix(cell_pert_fraction): + if cell_pert_fraction<0: + raise RuntimeError('cell_pert_fraction can not be negative') + e0 = np.random.rand(6) + e = e0 * 2 *cell_pert_fraction - cell_pert_fraction + cell_pert_matrix = np.array( + [[1+e[0], 0.5 * e[5], 0.5 * e[4]], + [0.5 * e[5], 1+e[1], 0.5 * e[3]], + [0.5 * e[4], 0.5 * e[3], 1+e[2]]] + ) + return cell_pert_matrix + +def get_atom_perturb_vector(atom_pert_distance, atom_pert_style='normal'): + random_vector = None + if atom_pert_distance < 0: + raise RuntimeError('atom_pert_distance can not be negative') + + if atom_pert_style == 'normal': + e = np.random.randn(3) + random_vector=(atom_pert_distance/np.sqrt(3))*e + elif atom_pert_style == 'uniform': + e = np.random.randn(3) + while np.linalg.norm(e) < 0.1: + e = np.random.randn(3) + random_unit_vector = e/np.linalg.norm(e) + v0 = np.random.rand(1) + v = np.power(v0,1/3) + random_vector = atom_pert_distance*v*random_unit_vector + elif atom_pert_style == 'const' : + e = np.random.randn(3) + while np.linalg.norm(e) < 0.1: + e = np.random.randn(3) + random_unit_vector = e/np.linalg.norm(e) + random_vector = atom_pert_distance*random_unit_vector + else: + raise RuntimeError('unsupported options atom_pert_style={}'.format(atom_pert_style)) + return random_vector class LabeledSystem (System): ''' @@ -622,6 +817,7 @@ def __init__ (self, - ``gaussian/log``: gaussian logs - ``gaussian/md``: gaussian ab initio molecular dynamics - ``cp2k/output``: cp2k output file + - ``cp2k/aimd_output``: cp2k aimd output dir(contains *pos*.xyz and *.log file) type_map : list of str Needed by formats deepmd/raw and deepmd/npy. Maps atom type to name. The atom with type `ii` is mapped to `type_map[ii]`. @@ -664,6 +860,8 @@ def __init__ (self, self.from_gaussian_log(file_name, md=True) elif fmt == 'cp2k/output': self.from_cp2k_output(file_name) + elif fmt == 'cp2k/aimd_output': + self.from_cp2k_aimd_output(file_dir=file_name) else : raise RuntimeError('unknow data format ' + fmt) @@ -707,6 +905,14 @@ def has_virial(self) : # return ('virials' in self.data) and (len(self.data['virials']) > 0) return ('virials' in self.data) + + def from_cp2k_aimd_output(self, file_dir): + xyz_file=glob.glob("{}/*pos*.xyz".format(file_dir))[0] + log_file=glob.glob("{}/*.log".format(file_dir))[0] + for info_dict in Cp2kSystems(log_file, xyz_file): + l = LabeledSystem(data=info_dict) + self.append(l) + def from_vasp_xml(self, file_name, begin = 0, step = 1) : self.data['atom_names'], \ self.data['atom_types'], \ @@ -834,6 +1040,7 @@ def from_gaussian_log(self, file_name, md=False): self.data = dpdata.gaussian.log.to_system_data(file_name, md=md) except AssertionError: self.data['energies'], self.data['forces']= [], [] + self.data['nopbc'] = True def from_cp2k_output(self, file_name) : @@ -1061,7 +1268,7 @@ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) : def check_System(data): keys={'atom_names','atom_numbs','cells','coords','orig','atom_types'} assert( isinstance(data,dict) ) - assert( set(data.keys())==keys ) + assert( keys.issubset(set(data.keys())) ) if len(data['coords']) > 0 : assert( len(data['coords'][0])==len(data['atom_types'])==sum(data['atom_numbs']) ) else : diff --git a/dpdata/vasp/__init__.py b/dpdata/vasp/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/tests/comp_sys.py b/tests/comp_sys.py index c53e14a51..8148e985a 100644 --- a/tests/comp_sys.py +++ b/tests/comp_sys.py @@ -58,6 +58,9 @@ def test_coord(self): places = self.places, msg = 'coord[%d][%d][%d] failed' % (ff,ii,jj)) + def test_nopbc(self): + self.assertEqual(self.system_1.nopbc, self.system_2.nopbc) + class CompLabeledSys (CompSys) : def test_energy(self) : @@ -97,4 +100,12 @@ def test_virial(self) : places = self.v_places, msg = 'virials[%d][%d][%d] failed' % (ff,ii,jj)) - +class IsPBC: + def test_is_pbc(self): + self.assertFalse(self.system_1.nopbc) + self.assertFalse(self.system_2.nopbc) + +class IsNoPBC: + def test_is_nopbc(self): + self.assertTrue(self.system_1.nopbc) + self.assertTrue(self.system_2.nopbc) diff --git a/tests/cp2k/aimd/coord.inc b/tests/cp2k/aimd/coord.inc new file mode 100644 index 000000000..0d8ed2a6a --- /dev/null +++ b/tests/cp2k/aimd/coord.inc @@ -0,0 +1,132 @@ + H 8.952797 9.523891 6.834498 + H 6.498623 1.465811 7.461476 + H 1.802104 6.443193 7.737154 + H 6.026557 5.139892 7.451687 + H 9.555537 9.168684 8.245566 + H 5.086122 1.750303 8.138474 + H 6.153436 3.729994 8.081213 + H 7.500876 8.844710 8.447625 + H 3.257230 6.226875 8.249061 + H 10.347343 2.068494 8.299805 + H 7.318487 7.449361 9.138426 + H 7.912738 5.447264 8.651730 + H 9.741755 3.224475 9.148382 + H 9.696946 7.240180 9.276467 + H 3.967794 0.525419 9.798147 + H 1.715060 3.398647 9.576735 + H 3.373479 1.966717 9.711748 + H 11.072558 7.954330 9.770082 + H 4.895864 5.373405 9.502802 + H 3.497480 4.938567 10.052435 + H 8.721783 5.252923 9.938822 + H 5.849387 8.910247 10.057023 + H 3.016764 7.444092 10.294122 + H 9.280502 9.176715 10.535702 + H 7.858849 9.153906 11.133965 + H 7.986650 3.033881 10.675968 + H 1.834351 3.231361 11.097070 + H 6.118946 0.948169 10.941198 + H 7.622106 1.027207 11.211985 + H 9.435564 3.153100 11.298905 + H 2.343684 -0.473902 11.254611 + H 5.483447 8.611905 11.534187 + H 2.143332 7.721526 11.584961 + H 3.269813 4.314981 12.097488 + H 6.405057 2.975006 12.172046 + H 1.047718 1.557454 11.987237 + H 2.962360 0.079065 12.556430 + H 6.903960 4.353920 12.707364 + H 0.015349 2.167285 12.993731 + H 9.492398 9.283543 12.839217 + H 4.876571 9.277822 13.300927 + H 4.491919 4.298588 13.031157 + H 1.314425 8.312767 13.449244 + H 1.684344 6.818888 13.511481 + H 1.788588 4.662438 13.865555 + H 5.416727 6.956404 13.622165 + H 9.927284 10.037646 14.129996 + H 6.739745 7.730543 13.793103 + H 3.394979 1.452172 14.371626 + H 0.334350 4.783913 14.524879 + H 3.309771 2.988917 14.352508 + H 8.334372 1.472729 14.245256 + H 6.380254 2.399484 14.129955 + H 5.797017 0.930689 14.230488 + H 4.449197 9.557363 14.735265 + H 9.351941 2.411141 14.952935 + O 8.871117 9.739342 7.794317 + O 5.793626 2.135827 7.531872 + O 2.725832 6.400405 7.434052 + O 6.231387 4.702548 8.307832 + O 10.503422 2.990054 8.575289 + O 6.832685 8.272449 8.919010 + O 8.614116 5.888689 9.191986 + O 3.845336 1.278261 9.187856 + O 10.161647 8.110641 9.370060 + O 4.091498 5.720115 9.960928 + O 2.379245 3.494241 10.317945 + O 2.225802 7.938866 10.596282 + O 8.713190 3.669513 10.845205 + O 5.381264 9.309910 10.850186 + O 8.704195 9.639287 11.209291 + O 6.831355 1.610513 11.113332 + O 2.386256 0.340940 11.807714 + O 0.516218 2.381379 12.159925 + O 6.229130 3.668806 12.864479 + O 3.504593 4.348522 13.041879 + O 6.049974 7.523179 13.116584 + O 2.040987 7.687175 13.210356 + O 9.900173 9.135620 13.734691 + O 4.449150 9.985783 13.834496 + O 1.108684 5.291520 14.179615 + O 9.303835 1.620825 14.350502 + O 6.487393 1.538073 14.610991 + O 3.240864 2.215917 14.957233 +Cu 0.000000 0.000000 1.400000 +Cu 2.560622 0.000000 1.400000 +Cu 5.121244 0.000000 1.400000 +Cu 7.681867 0.000000 1.400000 +Cu 0.000000 2.560622 1.400000 +Cu 2.560622 2.560622 1.400000 +Cu 5.121244 2.560622 1.400000 +Cu 7.681867 2.560622 1.400000 +Cu 0.000000 5.121244 1.400000 +Cu 2.560622 5.121244 1.400000 +Cu 5.121244 5.121244 1.400000 +Cu 7.681867 5.121244 1.400000 +Cu 0.000000 7.681867 1.400000 +Cu 2.560622 7.681867 1.400000 +Cu 5.121244 7.681867 1.400000 +Cu 7.681867 7.681867 1.400000 +Cu 1.280311 1.280311 3.210631 +Cu 3.840933 1.280311 3.210631 +Cu 6.401555 1.280311 3.210631 +Cu 8.962178 1.280311 3.210631 +Cu 1.280311 3.840933 3.210631 +Cu 3.840933 3.840933 3.210631 +Cu 6.401555 3.840933 3.210631 +Cu 8.962178 3.840933 3.210631 +Cu 1.280311 6.401555 3.210631 +Cu 3.840933 6.401555 3.210631 +Cu 6.401555 6.401555 3.210631 +Cu 8.962178 6.401555 3.210631 +Cu 1.280311 8.962178 3.210631 +Cu 3.840933 8.962178 3.210631 +Cu 6.401555 8.962178 3.210631 +Cu 8.962178 8.962178 3.210631 +Cu -0.036296 0.035664 4.996909 +Cu 2.520855 0.034382 5.028334 +Cu 5.081153 0.035111 5.007476 +Cu 7.639966 0.040634 4.987824 +Cu 0.039897 2.595141 5.032881 +Cu 2.598243 2.529957 5.008070 +Cu 5.161629 2.600062 5.059881 +Cu 7.727942 2.599403 5.001081 +Cu -0.038569 5.091749 5.009267 +Cu 2.595482 5.084765 5.057830 +Cu 5.151125 5.160971 4.992981 +Cu 7.646001 5.162257 5.036206 +Cu 0.037022 7.647075 5.005715 +Cu 2.601974 7.722328 5.045631 +Cu 5.163970 7.721760 5.031092 +Cu 7.721644 7.720984 5.013251 diff --git a/tests/cp2k/aimd/cp2k-pos-1.xyz b/tests/cp2k/aimd/cp2k-pos-1.xyz new file mode 100644 index 000000000..158a0c0a3 --- /dev/null +++ b/tests/cp2k/aimd/cp2k-pos-1.xyz @@ -0,0 +1,402 @@ + 132 + i = 0, time = 0.000, E = -2791.8673570370 + 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-0.0001388324 + H 0.0008464899 -0.0007026632 0.0007662455 + H -0.0000166696 0.0014698194 0.0008337244 + H -0.0000442715 -0.0000426033 0.0002937911 + H -0.0008114379 0.0001554464 -0.0010298817 + H -0.0007575316 -0.0004320480 -0.0004220362 + H 0.0009342970 -0.0005625925 -0.0005105201 + O 0.0003293286 -0.0000842335 0.0002593924 + O 0.0000311540 -0.0000198857 0.0002711850 + O 0.0000631400 -0.0000784543 -0.0000769579 + O -0.0000973908 0.0001204228 0.0002135487 + O 0.0000800659 -0.0001781209 0.0000531603 + O -0.0000386688 0.0000316107 -0.0000527182 + O 0.0001732330 -0.0001403900 0.0001529406 + O -0.0001800941 0.0001754044 -0.0002328883 + O 0.0000229508 -0.0001361381 0.0002601258 + O -0.0001476250 0.0001488546 0.0002419702 + O 0.0002220309 0.0001369924 0.0002994978 + O 0.0000731785 0.0000599772 0.0000470957 + O 0.0001745743 0.0000558329 -0.0004355060 + O 0.0001334078 0.0001750641 0.0004198694 + O -0.0000094741 -0.0001554715 -0.0000769174 + O 0.0000886649 -0.0003216828 0.0001263340 + O -0.0001259159 0.0002732738 -0.0001341932 + O -0.0001781580 -0.0000971521 -0.0000645257 + O -0.0001516559 -0.0003242220 -0.0000623913 + O -0.0001862961 -0.0002603251 0.0003362091 + O -0.0001147796 0.0000152433 -0.0002445541 + O 0.0000631475 -0.0000731061 -0.0002105931 + O 0.0000229579 0.0003952468 -0.0001091056 + O -0.0000917250 0.0001311876 0.0003823091 + O -0.0003757360 0.0000694658 -0.0001769032 + O -0.0000185904 -0.0002856210 0.0000117542 + O -0.0001247078 0.0002085100 0.0001513175 + O -0.0002019359 -0.0000793152 -0.0000833695 + Cu -0.0000452137 0.0000486030 0.0000961573 + Cu -0.0000199218 0.0001504544 -0.0000095879 + Cu 0.0000697098 -0.0000704858 0.0000617958 + Cu 0.0001484868 0.0001072982 -0.0000916793 + Cu -0.0000333331 0.0000574137 -0.0000190547 + Cu -0.0000706403 0.0000007292 -0.0000930973 + Cu 0.0000358010 0.0000180944 0.0000119368 + Cu -0.0000427213 0.0000059962 -0.0001770590 + Cu -0.0000401291 0.0000648313 -0.0000829819 + Cu -0.0001060333 0.0000233844 0.0001292016 + Cu 0.0000256814 0.0000252249 -0.0000145063 + Cu 0.0000646747 0.0000485347 -0.0001318161 + Cu 0.0000282538 0.0000695178 -0.0000763153 + Cu -0.0000150905 0.0000596225 0.0000050501 + Cu -0.0000095191 -0.0000841132 0.0000229068 + Cu -0.0001111846 -0.0000759998 -0.0000348889 + Cu 0.0000925625 -0.0000701164 -0.0000283459 + Cu 0.0000158722 -0.0000986981 -0.0000281223 + Cu 0.0000282867 -0.0000299432 -0.0000018063 + Cu 0.0002484820 0.0000922451 0.0000105611 + Cu -0.0001658051 0.0000517368 0.0001438175 + Cu 0.0000836881 -0.0001882566 0.0001368114 + Cu -0.0001570594 0.0000971785 -0.0000083909 + Cu -0.0000242055 0.0000073849 0.0000806168 + Cu 0.0001040208 -0.0000398423 0.0001137105 + Cu 0.0000912101 -0.0001196551 -0.0000385427 + Cu 0.0001234735 0.0001317162 0.0000790942 + Cu -0.0002636263 -0.0000595389 0.0000048457 + Cu 0.0000278592 -0.0000177437 0.0000980127 + Cu -0.0002177205 0.0001056148 -0.0001934752 + Cu 0.0000667295 -0.0000136684 -0.0001259048 + Cu -0.0000083359 -0.0000922386 -0.0000251294 + Cu 0.0000577403 0.0000820843 0.0000293456 + Cu -0.0000125219 0.0000667174 -0.0001514762 + Cu 0.0001231619 -0.0000800089 0.0000342450 + Cu 0.0000291633 -0.0000440385 0.0000647704 + Cu -0.0000187742 -0.0000887488 0.0000466911 + Cu 0.0000029631 -0.0000866068 -0.0000125627 + Cu 0.0000339075 0.0001718319 -0.0000571336 + Cu -0.0000854669 0.0000283685 -0.0000517992 + Cu 0.0001001614 -0.0000403887 0.0001146940 + Cu -0.0000980672 -0.0001292204 -0.0000973582 + Cu 0.0000360627 -0.0000247168 0.0000250778 + Cu 0.0000931493 -0.0001327813 -0.0000921738 + Cu -0.0000529727 -0.0001031971 0.0000688976 + Cu -0.0001093150 0.0001372915 0.0000210114 + Cu -0.0000185646 -0.0000295286 0.0000033851 + Cu 0.0001739177 0.0001016076 -0.0000939663 diff --git a/tests/cp2k/aimd/cp2k.inp b/tests/cp2k/aimd/cp2k.inp new file mode 100644 index 000000000..0dc9bb276 --- /dev/null +++ b/tests/cp2k/aimd/cp2k.inp @@ -0,0 +1,186 @@ +@SET DATAPATH /public/source/cp2k-6.1.0/data/ + + +&FORCE_EVAL + METHOD Quickstep + &DFT + BASIS_SET_FILE_NAME ${DATAPATH}/BASIS_MOLOPT +# POTENTIAL_FILE_NAME ./rr_pot + POTENTIAL_FILE_NAME ${DATAPATH}/GTH_POTENTIALS + WFN_RESTART_FILE_NAME ./cp2k-RESTART.wfn +# PLUS_U_METHOD mulliken_charges +# CHARGE +2 + UKS T +# MULTIPLICITY 1 + &MGRID + CUTOFF 350 + &END MGRID + &QS + WF_INTERPOLATION ASPC + EXTRAPOLATION_ORDER 3 + &END QS +# &POISSON +# PERIODIC NONE +# POISSON_SOLVER MT +# &MT +# ALPHA 7.0 +# REL_CUTOFF 1.2 +# &END MT +# &END POISSON + &SCF + SCF_GUESS RESTART + EPS_SCF 1.0E-6 + MAX_SCF 500 + ADDED_MOS 500 + CHOLESKY INVERSE + &SMEAR ON + METHOD FERMI_DIRAC + ELECTRONIC_TEMPERATURE [K] 300 + &END SMEAR + &DIAGONALIZATION + ALGORITHM STANDARD + EPS_ADAPT 0.01 + &END DIAGONALIZATION + &MIXING + METHOD BROYDEN_MIXING + ALPHA 0.1 + BETA 1.5 + NBROYDEN 8 + &END MIXING + &END SCF + &XC + &XC_FUNCTIONAL PBE + &END XC_FUNCTIONAL + &END XC + &PRINT + &MULLIKEN SILENT + FILENAME =Mull.mulliken + &EACH + MD 5 + &END EACH + &END MULLIKEN + +# &E_DENSITY_CUBE +# FILENAME Dentity_maybeSpin.cube +# &END E_DENSITY_CUBE +# &MO_CUBES +# NLUMO 1 +# FILENAME MO.cube +# &END MO_CUBES + &END PRINT + &END DFT + &PRINT + &FORCES ON + &END FORCES + &END PRINT + &SUBSYS + &CELL + ABC 10.242489 10.242489 23.0 + ALPHA_BETA_GAMMA 90 90 90 + &END CELL + &COORD + @INCLUDE 'coord.inc' + &END COORD +# &TOPOLOGY +# &CENTER_COORDINATES +# &END CENTER_COORDINATES +# &END TOPOLOGY + &KIND C + BASIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q4 + &END KIND + &KIND O + BASIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q6 + &END KIND + &KIND H + BASIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q1 + &END KIND + &KIND Cu + BaSIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q11 + &END KIND + &KIND Al + BaSIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q3 + &END KIND + &KIND Pt + BASIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q18 + &END KIND + &KIND Pd + BaSIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q18 + &END KIND + &KIND Au + BaSIS_SET DZVP-MOLOPT-SR-GTH + POTENTIAL GTH-PBE-q11 + &END KIND + &END SUBSYS +&END FORCE_EVAL +&GLOBAL +# FFTLIB FFTSG + PROJECT cp2k + # RUN_TYPE GEO_OPT +# RUN_TYPE ENERGY + RUN_TYPE MD + PRINT_LEVEL LOW +&END GLOBAL + &MOTION + &MD + ENSEMBLE NVT + STEPS 2 + TIMESTEP 0.5 + TEMPERATURE 300.0 +# ANNEALING 0.98 +# use in NVT ensemble + &THERMOSTAT + TYPE NOSE +# REGION MASSIVE + &NOSE + LENGTH 3 + YOSHIDA 3 + MTS 2 + TIMECON [wavenumber_t] 1000 + &END NOSE + &END THERMOSTAT + &END MD + &GEO_OPT + MAX_ITER 400 + OPTIMIZER LBFGS +# OPTIMIZER BFGS +# OPTIMIZER CG + MAX_FORCE 6.0E-4 + &LBFGS + MAX_H_RANK 30 + &END LBFGS +# &CG +# &LINE_SEARCH +# TYPE 2PNT +# &END LINE_SEARCH +# &END CG + &END GEO_OPT + &PRINT + &TRAJECTORY + &EACH + MD 1 + &END EACH + &END TRAJECTORY + &VELOCITIES + &EACH + MD 1 + &END EACH + &END VELOCITIES + &RESTART_HISTORY + &EACH + MD 5 + &END EACH + &END RESTART_HISTORY + &END PRINT + &CONSTRAINT + &FIXED_ATOMS + LIST 139..170 + &END FIXED_ATOMS + &END CONSTRAINT +&END MOTION diff --git a/tests/cp2k/aimd/cp2k.log b/tests/cp2k/aimd/cp2k.log new file mode 100644 index 000000000..c9e081ca5 --- /dev/null +++ b/tests/cp2k/aimd/cp2k.log @@ -0,0 +1,1089 @@ + DBCSR| Multiplication driver BLAS + DBCSR| Multrec recursion limit 512 + DBCSR| Multiplication stack size 1000 + DBCSR| Maximum elements for images UNLIMITED + DBCSR| Multiplicative factor virtual images 1 + DBCSR| Multiplication size stacks 3 + DBCSR| Number of 3D layers SINGLE + DBCSR| Use MPI memory allocation T + DBCSR| Use RMA algorithm F + DBCSR| Use Communication thread T + DBCSR| Communication thread load 87 + + + **** **** ****** ** PROGRAM STARTED AT 2019-12-21 14:06:43.310 + ***** ** *** *** ** PROGRAM STARTED ON node16 + ** **** ****** PROGRAM STARTED BY nxu + ***** ** ** ** ** PROGRAM PROCESS ID 287845 + **** ** ******* ** PROGRAM STARTED IN /public/home/apclab/nxu/uk/cu100-h2o- + aimd-test_force + + CP2K| version string: CP2K version 6.1 + CP2K| source code revision number: svn:18464 + CP2K| cp2kflags: libint fftw3 libxc elpa=201705 elpa_qr parallel mpi3 scalapack + CP2K| has_no_shared_glibc libderiv_max_am1=6 libint_max_am=7 max_contr=4 mkl + CP2K| is freely available from https://www.cp2k.org/ + CP2K| Program compiled at Tue May 7 00:08:04 CST 2019 + CP2K| Program compiled on tc6000 + CP2K| Program compiled for Linux-x86-64-intel + CP2K| Data directory path /public/source/cp2k-6.1.0/data + CP2K| Input file name cp2k.inp + + GLOBAL| Force Environment number 1 + GLOBAL| Basis set file name /public/source/cp2k-6.1.0/data//BASIS_MO + GLOBAL| Potential file name /public/source/cp2k-6.1.0/data//GTH_POTE + GLOBAL| MM Potential file name MM_POTENTIAL + GLOBAL| Coordinate file name __STD_INPUT__ + GLOBAL| Method name CP2K + GLOBAL| Project name cp2k + GLOBAL| Preferred FFT library FFTW3 + GLOBAL| Preferred diagonalization lib. SL + GLOBAL| Run type MD + GLOBAL| All-to-all communication in single precision F + GLOBAL| FFTs using library dependent lengths F + GLOBAL| Global print level LOW + GLOBAL| Total number of message passing processes 24 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + GLOBAL| CPU model name : Intel(R) Xeon(R) Silver 4116 CPU @ 2.10GHz + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 131449580 131449580 131449580 131449580 + MEMORY| MemFree 14125636 14125636 14125636 14125636 + MEMORY| Buffers 427256 427256 427256 427256 + MEMORY| Cached 113148472 113148472 113148472 113148472 + MEMORY| Slab 1079332 1079332 1079332 1079332 + MEMORY| SReclaimable 850496 850496 850496 850496 + MEMORY| MemLikelyFree 128551860 128551860 128551860 128551860 + + + GENERATE| Preliminary Number of Bonds generated: 0 + GENERATE| Achieved consistency in connectivity generation. + + ******************************************************************************* + ******************************************************************************* + ** ** + ** ##### ## ## ** + ** ## ## ## ## ## ** + ** ## ## ## ###### ** + ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** + ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** + ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** + ** ## ### ## ## ## ## ## ## ## ## ## ## ** + ** ####### ##### ## ##### ## ## #### ## ##### ## ** + ** ## ## ** + ** ** + ** ... make the atoms dance ** + ** ** + ** Copyright (C) by CP2K developers group (2000 - 2018) ** + ** ** + ******************************************************************************* + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 3 + - Atoms: 132 + - Shell sets: 132 + - Shells: 644 + - Primitive Cartesian functions: 708 + - Cartesian basis functions: 2112 + - Spherical basis functions: 1844 + + Maximum angular momentum of- Orbital basis functions: 3 + - Local part of the GTH pseudopotential: 2 + - Non-local part of the GTH pseudopotential: 4 + + + SCF PARAMETERS Density guess: RESTART + -------------------------------------------------------- + max_scf: 500 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + eps_scf: 1.00E-06 + eps_scf_history: 0.00E+00 + eps_diis: 1.00E-01 + eps_eigval: 1.00E-05 + -------------------------------------------------------- + level_shift [a.u.]: 0.00 + added MOs 500 500 + -------------------------------------------------------- + Mixing method: BROYDEN_MIXING + charge density mixing in g-space + -------------------------------------------------------- + Smear method: FERMI_DIRAC + Electronic temperature [K]: 300.0 + Electronic temperature [a.u.]: 9.50E-04 + Accuracy threshold: 1.00E-10 + -------------------------------------------------------- + No outer SCF + + MD| Molecular Dynamics Protocol + MD| Ensemble Type NVT + MD| Number of Time Steps 2 + MD| Time Step [fs] 0.50 + MD| Temperature [K] 300.00 + MD| Temperature tolerance [K] 0.00 + MD| Constraints activated + MD| Tolerance for shake 0.1000E-05 + MD| Print MD information every 1 step(s) + MD| File type Print frequency[steps] File names + MD| Coordinates 1 cp2k-pos-1.xyz + MD| Velocities 1 cp2k-vel-1.xyz + MD| Energies 1 cp2k-1.ener + MD| Dump 20 cp2k-1.restart + + ROT| Rotational Analysis Info + ROT| Principal axes and moments of inertia in atomic units: + ROT| 1 2 3 + ROT| EIGENVALUES 0.381434679E+09 0.447122074E+09 0.459917132E+09 + ROT| X 0.452286651 0.438333257 -0.776724366 + ROT| Y 0.378310829 0.694372806 0.612149756 + ROT| Z 0.807661874 -0.570710401 0.148229333 + ROT| Numer of Rotovibrational vectors: 6 + + Calculation of degrees of freedom + Number of atoms: 132 + Number of Intramolecular constraints: 0 + Number of Intermolecular constraints: 0 + Invariants(translation + rotations): 3 + Degrees of freedom: 393 + + + Restraints Information + Number of Intramolecular restraints: 0 + Number of Intermolecular restraints: 0 + + THERMOSTAT| Thermostat Info for PARTICLES + THERMOSTAT| Type of thermostat Nose-Hoover-Chains + THERMOSTAT| Nose-Hoover-Chain length 3 + THERMOSTAT| Nose-Hoover-Chain time constant [ fs] 33.36 + THERMOSTAT| Order of Yoshida integrator 3 + THERMOSTAT| Number of multiple time steps 2 + THERMOSTAT| Initial Potential Energy 0.000000 + THERMOSTAT| Initial Kinetic Energy 0.000475 + THERMOSTAT| End of Thermostat Info for PARTICLES + + ************************** Velocities initialization ************************** + Initial Temperature 300.00 K + COM velocity: 0.000000000000 -0.000000000000 -0.000000000000 + ******************************************************************************* + + + Spin 1 + + Number of electrons: 376 + Number of occupied orbitals: 376 + Number of molecular orbitals: 876 + + Spin 2 + + Number of electrons: 376 + Number of occupied orbitals: 376 + Number of molecular orbitals: 876 + + Number of orbital functions: 1844 + Number of independent orbital functions: 1844 + + Extrapolation method: initial_guess + + + SCF WAVEFUNCTION OPTIMIZATION + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 NoMix/Diag. 0.10E+00 4.0 0.00000473 -2791.8631880279 -2.79E+03 + 2 Broy./Diag. 0.10E+00 5.5 0.00000176 -2791.8673978615 -4.21E-03 + 3 Broy./Diag. 0.10E+00 5.6 0.00000278 -2791.8673824629 1.54E-05 + 4 Broy./Diag. 0.10E+00 5.5 0.00000045 -2791.8673628826 1.96E-05 + + *** SCF run converged in 4 steps *** + + + Electronic density on regular grids: -751.9999998245 0.0000001755 + Core density on regular grids: 751.9999999308 -0.0000000692 + Total charge density on r-space grids: 0.0000001062 + Total charge density g-space grids: 0.0000001062 + + Overlap energy of the core charge distribution: 0.00000127858088 + Self energy of the core charge distribution: -4333.05345429107729 + Core Hamiltonian energy: 1407.49397995580830 + Hartree energy: 624.30200292764744 + Exchange-correlation energy: -490.60572373272350 + Electronic entropic energy: -0.00416901691843 + Fermi energy: -0.00533043279024 + + Total energy: -2791.86736288261091 + + Integrated absolute spin density : 0.0000000000 + WARNING: S**2 computation does not yet treat fractional occupied orbitals + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -2791.867357036983321 + + + ATOMIC FORCES in [a.u.] + + # Atom Kind Element X Y Z + 1 1 H -0.00022986 -0.00013577 -0.00049300 + 2 1 H 0.00004574 0.00001286 -0.00021297 + 3 1 H 0.00017833 0.00006201 -0.00019739 + 4 1 H 0.00009277 0.00001450 -0.00017004 + 5 1 H -0.00011411 0.00024873 -0.00016097 + 6 1 H 0.00032677 0.00015892 -0.00034887 + 7 1 H -0.00001396 -0.00032189 -0.00016679 + 8 1 H 0.00051501 0.00043671 -0.00048215 + 9 1 H -0.00050559 0.00003640 -0.00034967 + 10 1 H -0.00000820 0.00006898 -0.00008688 + 11 1 H 0.00024747 -0.00004379 -0.00035656 + 12 1 H 0.00000939 -0.00015928 -0.00035535 + 13 1 H 0.00025243 -0.00016696 -0.00029669 + 14 1 H 0.00025189 0.00021719 -0.00013519 + 15 1 H -0.00049917 0.00056415 -0.00030765 + 16 1 H -0.00006814 0.00000543 -0.00014073 + 17 1 H -0.00003630 0.00004326 0.00010699 + 18 1 H -0.00059591 0.00008771 -0.00019057 + 19 1 H 0.00008307 -0.00030089 -0.00049754 + 20 1 H -0.00031704 -0.00032945 0.00014050 + 21 1 H 0.00017859 -0.00013881 -0.00037607 + 22 1 H 0.00125447 -0.00068555 -0.00189666 + 23 1 H -0.00059716 -0.00010911 -0.00062913 + 24 1 H -0.00033447 -0.00001053 0.00016315 + 25 1 H 0.00134965 0.00074573 -0.00110083 + 26 1 H -0.00015874 -0.00023377 -0.00007275 + 27 1 H 0.00028330 0.00001068 0.00017396 + 28 1 H 0.00067342 0.00141108 0.00016600 + 29 1 H 0.00015297 -0.00010669 0.00022029 + 30 1 H 0.00033031 -0.00030660 -0.00024616 + 31 1 H -0.00057924 0.00017784 0.00003946 + 32 1 H -0.00134178 0.00338837 -0.00521905 + 33 1 H -0.00086135 0.00013421 0.00050741 + 34 1 H 0.00043448 0.00041063 -0.00011188 + 35 1 H -0.00017342 -0.00078558 0.00079126 + 36 1 H 0.00009936 -0.00025170 0.00063389 + 37 1 H -0.00276891 0.00154205 -0.00091328 + 38 1 H -0.00004718 -0.00215183 -0.00191570 + 39 1 H 0.00195565 -0.00071401 -0.00186039 + 40 1 H 0.00301162 0.00004608 0.00523141 + 41 1 H -0.00181602 0.00335717 -0.00019462 + 42 1 H -0.00108395 -0.00390451 -0.00072994 + 43 1 H -0.00455805 0.00233387 0.00081755 + 44 1 H -0.00059661 -0.00010012 0.00266729 + 45 1 H -0.00063848 -0.00268972 0.00298896 + 46 1 H 0.00481741 0.00519923 -0.01047650 + 47 1 H -0.00066110 -0.00654027 -0.00124201 + 48 1 H -0.00465129 -0.00064975 -0.01097880 + 49 1 H -0.00045417 0.00482931 0.00283734 + 50 1 H 0.01795602 0.00842007 -0.00822459 + 51 1 H -0.00055227 -0.00634994 0.00125942 + 52 1 H -0.01229946 -0.00205148 0.00419137 + 53 1 H -0.00427695 -0.00823037 0.00520798 + 54 1 H 0.00758709 0.01008084 0.00423419 + 55 1 H -0.00656272 0.01162474 -0.01537368 + 56 1 H -0.00032438 -0.02057775 -0.00753751 + 57 2 O -0.00076334 0.00084962 0.00234418 + 58 2 O -0.00154238 0.00037972 0.00044361 + 59 2 O -0.00029387 -0.00050448 -0.00529572 + 60 2 O -0.00000652 0.00135884 -0.00050225 + 61 2 O 0.00102792 0.00012922 0.00503096 + 62 2 O -0.00035026 -0.00076088 0.00409273 + 63 2 O -0.00081690 0.00027615 0.00462918 + 64 2 O 0.00057463 -0.00045688 0.00466151 + 65 2 O -0.00009951 -0.00038935 0.00367089 + 66 2 O 0.00087082 0.00052849 -0.00183506 + 67 2 O -0.00017490 -0.00007043 -0.00462987 + 68 2 O 0.00198328 0.00009674 0.00053201 + 69 2 O 0.00119937 0.00020623 -0.00678448 + 70 2 O 0.00015640 -0.00172215 0.00201285 + 71 2 O -0.00196795 -0.00134482 0.00435407 + 72 2 O 0.00015426 -0.00230905 -0.00192880 + 73 2 O 0.00129758 -0.00117969 0.00137391 + 74 2 O -0.00098835 -0.00032197 0.00411925 + 75 2 O 0.00083408 0.00654717 -0.00141020 + 76 2 O 0.00189940 0.00572146 -0.00288006 + 77 2 O 0.00117347 -0.00837967 0.02230425 + 78 2 O 0.00407062 -0.00166907 -0.00429214 + 79 2 O -0.00029109 0.00358448 -0.00765050 + 80 2 O 0.00389290 -0.01748412 0.01615020 + 81 2 O -0.01515586 -0.00651340 0.00462606 + 82 2 O 0.00704074 0.02325146 0.00801056 + 83 2 O 0.00564534 -0.00125716 -0.00741703 + 84 2 O -0.00215229 0.00210252 -0.00067511 + 85 3 Cu 0.00018081 -0.00002625 -0.00004173 + 86 3 Cu 0.00002598 0.00008208 -0.00242849 + 87 3 Cu -0.00007526 0.00009648 -0.00142154 + 88 3 Cu -0.00000872 -0.00009519 0.00026886 + 89 3 Cu 0.00007205 -0.00008748 -0.00205778 + 90 3 Cu -0.00003253 -0.00009703 -0.00165078 + 91 3 Cu -0.00002554 -0.00015342 -0.00194239 + 92 3 Cu -0.00019180 0.00007334 -0.00098987 + 93 3 Cu 0.00001348 -0.00003689 -0.00167315 + 94 3 Cu 0.00011457 0.00020464 -0.00132377 + 95 3 Cu -0.00023804 -0.00000172 -0.00022774 + 96 3 Cu 0.00017614 -0.00001293 -0.00152236 + 97 3 Cu -0.00008182 0.00002499 -0.00106650 + 98 3 Cu 0.00009170 -0.00034197 -0.00164677 + 99 3 Cu -0.00017686 -0.00010567 -0.00210110 + 100 3 Cu -0.00001625 -0.00016813 -0.00160101 + 101 3 Cu -0.00048755 0.00084880 0.00298924 + 102 3 Cu 0.00111423 0.00115977 0.00225361 + 103 3 Cu -0.00135350 0.00240795 0.00323730 + 104 3 Cu 0.00039599 0.00181105 0.00310311 + 105 3 Cu 0.00156694 0.00103959 0.00447175 + 106 3 Cu 0.00100602 -0.00007888 0.00564324 + 107 3 Cu 0.00038440 -0.00060038 0.00266400 + 108 3 Cu -0.00026513 0.00083471 0.00304344 + 109 3 Cu 0.00249728 -0.00118908 0.00737516 + 110 3 Cu -0.00095036 0.00120971 0.00484766 + 111 3 Cu 0.00085824 0.00237740 0.00405029 + 112 3 Cu -0.00027653 -0.00008114 0.00288706 + 113 3 Cu 0.00052739 -0.00038939 0.00492108 + 114 3 Cu -0.00059129 -0.00016575 0.00521348 + 115 3 Cu -0.00019214 0.00068018 0.00244886 + 116 3 Cu 0.00059308 0.00012040 0.00268430 + 117 3 Cu -0.00073161 0.00090135 0.00031314 + 118 3 Cu 0.00042214 -0.00148108 -0.00002173 + 119 3 Cu 0.00000407 0.00011115 -0.00334710 + 120 3 Cu -0.00031805 0.00047811 0.00163103 + 121 3 Cu -0.00034882 -0.00128562 0.00091899 + 122 3 Cu -0.00009299 0.00008045 -0.00256815 + 123 3 Cu 0.00018747 0.00022483 0.00405435 + 124 3 Cu -0.00006993 0.00048854 -0.00333844 + 125 3 Cu 0.00010935 0.00026660 -0.00225980 + 126 3 Cu 0.00065710 -0.00061092 0.00096128 + 127 3 Cu 0.00193824 0.00061232 0.00007119 + 128 3 Cu 0.00126443 -0.00036529 0.00027645 + 129 3 Cu 0.00033193 -0.00017841 -0.00302791 + 130 3 Cu -0.00022105 0.00008591 0.00155020 + 131 3 Cu 0.00008569 -0.00044808 0.00032086 + 132 3 Cu -0.00008912 -0.00007169 -0.00147972 + SUM OF ATOMIC FORCES 0.00936265 0.00643956 0.03584699 0.03760497 + + MD_ENERGIES| Initialization proceeding + + + ******************************** GO CP2K GO! ********************************** + INITIAL POTENTIAL ENERGY[hartree] = -0.279186735704E+04 + INITIAL KINETIC ENERGY[hartree] = 0.186683764487E+00 + INITIAL TEMPERATURE[K] = 300.000 + INITIAL VOLUME[bohr^3] = 0.162830387070E+05 + INITIAL CELL LNTHS[bohr] = 0.1935550E+02 0.1935550E+02 0.4346370E+02 + INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.9000000E+02 + ******************************** GO CP2K GO! ********************************** + + Spin 1 + + Number of electrons: 376 + Number of occupied orbitals: 380 + Number of molecular orbitals: 876 + + Spin 2 + + Number of electrons: 376 + Number of occupied orbitals: 380 + Number of molecular orbitals: 876 + + Number of orbital functions: 1844 + Number of independent orbital functions: 1844 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 Broy./Diag. 0.10E+00 3.8 0.02159123 -2791.8462829580 -2.79E+03 + 2 Broy./Diag. 0.10E+00 5.5 0.00062121 -2791.8738228556 -2.75E-02 + 3 Broy./Diag. 0.10E+00 5.5 0.00400265 -2791.8704581787 3.36E-03 + 4 Broy./Diag. 0.10E+00 5.5 0.00015030 -2791.8446778939 2.58E-02 + 5 Broy./Diag. 0.10E+00 5.5 0.00048065 -2791.8626573391 -1.80E-02 + 6 Broy./Diag. 0.10E+00 5.5 0.00013594 -2791.8817959540 -1.91E-02 + 7 Broy./Diag. 0.10E+00 5.5 0.00010040 -2791.8685733048 1.32E-02 + 8 Broy./Diag. 0.10E+00 5.6 0.00009396 -2791.8616518463 6.92E-03 + 9 Broy./Diag. 0.10E+00 5.6 0.00008035 -2791.8695966824 -7.94E-03 + 10 Broy./Diag. 0.10E+00 5.6 0.00009527 -2791.8708531762 -1.26E-03 + 11 Broy./Diag. 0.10E+00 5.6 0.00001407 -2791.8652630149 5.59E-03 + 12 Broy./Diag. 0.10E+00 5.6 0.00005363 -2791.8655483836 -2.85E-04 + 13 Broy./Diag. 0.10E+00 5.6 0.00001076 -2791.8672762293 -1.73E-03 + 14 Broy./Diag. 0.10E+00 5.6 0.00002121 -2791.8658040279 1.47E-03 + 15 Broy./Diag. 0.10E+00 5.6 0.00003242 -2791.8639043304 1.90E-03 + 16 Broy./Diag. 0.10E+00 5.6 0.00000735 -2791.8634485766 4.56E-04 + 17 Broy./Diag. 0.10E+00 5.6 0.00001345 -2791.8640685356 -6.20E-04 + 18 Broy./Diag. 0.10E+00 5.6 0.00000859 -2791.8652349958 -1.17E-03 + 19 Broy./Diag. 0.10E+00 5.6 0.00001895 -2791.8648548701 3.80E-04 + 20 Broy./Diag. 0.10E+00 5.6 0.00000422 -2791.8641550955 7.00E-04 + 21 Broy./Diag. 0.10E+00 5.6 0.00000896 -2791.8640355856 1.20E-04 + 22 Broy./Diag. 0.10E+00 5.6 0.00000415 -2791.8640067752 2.88E-05 + 23 Broy./Diag. 0.10E+00 5.6 0.00000137 -2791.8640675132 -6.07E-05 + 24 Broy./Diag. 0.10E+00 5.6 0.00000290 -2791.8643916841 -3.24E-04 + 25 Broy./Diag. 0.10E+00 5.6 0.00000220 -2791.8648473760 -4.56E-04 + 26 Broy./Diag. 0.10E+00 5.6 0.00000201 -2791.8645612429 2.86E-04 + 27 Broy./Diag. 0.10E+00 5.6 0.00000081 -2791.8641977080 3.64E-04 + + *** SCF run converged in 27 steps *** + + + Electronic density on regular grids: -751.9999998286 0.0000001714 + Core density on regular grids: 751.9999999307 -0.0000000693 + Total charge density on r-space grids: 0.0000001021 + Total charge density g-space grids: 0.0000001021 + + Overlap energy of the core charge distribution: 0.00000133552913 + Self energy of the core charge distribution: -4333.05345429107729 + Core Hamiltonian energy: 1407.56629650839386 + Hartree energy: 624.25271166673599 + Exchange-correlation energy: -490.62558651522397 + Electronic entropic energy: -0.00416639933775 + Fermi energy: -0.00528076027334 + + Total energy: -2791.86419770804559 + + Integrated absolute spin density : 0.0000000000 + WARNING: S**2 computation does not yet treat fractional occupied orbitals + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -2791.864262781982688 + + + ATOMIC FORCES in [a.u.] + + # Atom Kind Element X Y Z + 1 1 H -0.00021479 0.00067600 0.00463602 + 2 1 H -0.00058016 0.00132010 -0.00013773 + 3 1 H -0.01262388 0.00067794 0.00253486 + 4 1 H -0.00138690 0.00346867 -0.00502344 + 5 1 H -0.00345562 0.00280934 -0.00309727 + 6 1 H 0.00165473 0.00169149 -0.00197578 + 7 1 H 0.00142536 0.00721786 0.00257009 + 8 1 H 0.00107038 -0.00127784 0.00046906 + 9 1 H 0.00416261 -0.00146555 0.00384818 + 10 1 H -0.00180364 -0.01165723 -0.00376846 + 11 1 H -0.00221948 0.00588912 -0.00253783 + 12 1 H 0.00290043 0.00113890 0.00254741 + 13 1 H 0.00633645 -0.00165707 -0.00465765 + 14 1 H -0.00397119 -0.00995294 -0.00083937 + 15 1 H -0.00140674 0.00253845 -0.00200065 + 16 1 H -0.00019689 0.00074006 -0.00216829 + 17 1 H 0.00182973 -0.00246982 -0.00189013 + 18 1 H -0.00209590 -0.00022029 -0.00027150 + 19 1 H 0.00368920 -0.00214102 -0.00272376 + 20 1 H -0.00044477 -0.00042014 -0.00102772 + 21 1 H 0.00073450 -0.00321761 0.00317859 + 22 1 H -0.00210997 0.00168775 0.00408038 + 23 1 H 0.01314480 -0.00799753 -0.00653788 + 24 1 H 0.00223613 -0.00200390 -0.00221315 + 25 1 H -0.01211882 -0.00704369 -0.00209666 + 26 1 H 0.00234440 0.00299332 0.00039711 + 27 1 H 0.00007060 -0.00032279 0.00249363 + 28 1 H 0.00635070 0.00489302 0.00119390 + 29 1 H 0.00777439 -0.00619947 0.00132604 + 30 1 H 0.00122686 -0.00065844 -0.00040964 + 31 1 H -0.00008392 -0.00455643 -0.00263935 + 32 1 H -0.00145725 0.00295753 -0.00558337 + 33 1 H -0.00195940 0.00065573 0.00339567 + 34 1 H -0.00094211 0.00047492 0.00371077 + 35 1 H 0.00099659 0.00027462 0.00075445 + 36 1 H 0.00512619 -0.00831137 -0.00078744 + 37 1 H -0.00303978 0.00070884 -0.00184117 + 38 1 H -0.00139022 -0.00421461 -0.00235979 + 39 1 H 0.00487207 -0.00030354 -0.00598967 + 40 1 H 0.00567993 -0.00006164 0.01180487 + 41 1 H -0.00540561 0.00950043 0.00411851 + 42 1 H 0.00156512 -0.00382695 0.00155110 + 43 1 H -0.00622471 0.00450056 0.00116055 + 44 1 H 0.00444517 0.01098625 -0.00106148 + 45 1 H -0.00378740 0.00120222 0.00458868 + 46 1 H -0.00268852 -0.00131545 -0.00524932 + 47 1 H -0.00138537 -0.01220652 -0.00443997 + 48 1 H 0.00103413 0.00124670 -0.00607690 + 49 1 H -0.00066927 0.00576712 0.00344085 + 50 1 H 0.01264274 0.00588311 -0.00598738 + 51 1 H 0.00003551 0.00140070 -0.00488471 + 52 1 H -0.01887139 -0.00454860 0.00261124 + 53 1 H -0.00430195 -0.00657263 0.00460886 + 54 1 H 0.01550239 0.01604420 0.00922541 + 55 1 H -0.00639507 0.01133036 -0.01335261 + 56 1 H 0.00066968 -0.01929850 -0.00627904 + 57 2 O 0.00139607 -0.00242090 0.00049877 + 58 2 O -0.00267347 -0.00175924 0.00309521 + 59 2 O 0.00773044 0.00045276 -0.01227401 + 60 2 O 0.00058955 -0.01018139 0.00210003 + 61 2 O -0.00333800 0.01374197 0.01359850 + 62 2 O 0.00175720 -0.00499770 0.00566105 + 63 2 O -0.00531281 0.00316316 -0.00235217 + 64 2 O 0.00051103 -0.00073576 0.00895021 + 65 2 O 0.00594084 0.01065802 0.00327673 + 66 2 O -0.00225691 0.00197710 0.00003778 + 67 2 O -0.00048099 -0.00109522 -0.00567576 + 68 2 O -0.01101459 0.00760549 0.00326791 + 69 2 O -0.00296332 -0.00311932 -0.00758647 + 70 2 O 0.00370201 -0.00384502 -0.00329503 + 71 2 O 0.00917698 0.00862816 0.00766411 + 72 2 O -0.01337812 0.00053039 -0.00339467 + 73 2 O 0.00181792 0.00362998 0.00452530 + 74 2 O -0.00861898 0.00771547 0.01008472 + 75 2 O 0.00179027 0.00905186 -0.00106772 + 76 2 O 0.00136516 0.00683091 -0.00960843 + 77 2 O 0.00316580 -0.00360086 0.01308553 + 78 2 O 0.00074047 -0.01504781 0.00009668 + 79 2 O -0.00244576 0.00800208 -0.01086906 + 80 2 O 0.00765837 -0.02350153 0.01056746 + 81 2 O -0.00589892 -0.00804755 0.00000088 + 82 2 O 0.01274151 0.02512189 0.00839910 + 83 2 O -0.00206703 -0.00945281 -0.01070272 + 84 2 O -0.00223901 -0.00655437 0.00485398 + 85 3 Cu 0.00013883 0.00007948 -0.00009788 + 86 3 Cu -0.00005759 0.00043724 -0.00251801 + 87 3 Cu 0.00015134 -0.00007751 -0.00146480 + 88 3 Cu 0.00038762 0.00015955 0.00038505 + 89 3 Cu -0.00001027 0.00013307 -0.00205574 + 90 3 Cu -0.00019150 0.00003251 -0.00156047 + 91 3 Cu 0.00000965 -0.00015101 -0.00193647 + 92 3 Cu -0.00027722 0.00015997 -0.00078245 + 93 3 Cu -0.00010376 0.00017003 -0.00168749 + 94 3 Cu -0.00011744 0.00020987 -0.00113106 + 95 3 Cu -0.00019894 0.00001782 -0.00021180 + 96 3 Cu 0.00026996 0.00003260 -0.00169544 + 97 3 Cu -0.00004310 0.00015789 -0.00102570 + 98 3 Cu 0.00002378 -0.00021821 -0.00163188 + 99 3 Cu -0.00025259 -0.00031613 -0.00209633 + 100 3 Cu -0.00023057 -0.00027107 -0.00164267 + 101 3 Cu -0.00030201 0.00083415 0.00297032 + 102 3 Cu 0.00126429 0.00101808 0.00225508 + 103 3 Cu -0.00116070 0.00237503 0.00325167 + 104 3 Cu 0.00070402 0.00196948 0.00308277 + 105 3 Cu 0.00131472 0.00101682 0.00421765 + 106 3 Cu 0.00098186 -0.00041794 0.00537199 + 107 3 Cu 0.00024164 -0.00039717 0.00248664 + 108 3 Cu -0.00037368 0.00084662 0.00284711 + 109 3 Cu 0.00250599 -0.00116918 0.00727046 + 110 3 Cu -0.00076613 0.00101942 0.00495356 + 111 3 Cu 0.00095073 0.00255639 0.00398568 + 112 3 Cu -0.00045799 -0.00021966 0.00279348 + 113 3 Cu 0.00041354 -0.00048721 0.00476631 + 114 3 Cu -0.00084481 -0.00010038 0.00543998 + 115 3 Cu -0.00013476 0.00069681 0.00257233 + 116 3 Cu 0.00066504 0.00004635 0.00262534 + 117 3 Cu -0.00108220 0.00043300 0.00022713 + 118 3 Cu 0.00049863 -0.00179007 -0.00024378 + 119 3 Cu -0.00047651 0.00031478 -0.00341442 + 120 3 Cu -0.00041608 0.00076680 0.00148417 + 121 3 Cu -0.00029993 -0.00109552 0.00096943 + 122 3 Cu -0.00007795 0.00038274 -0.00251773 + 123 3 Cu 0.00001991 -0.00070041 0.00418248 + 124 3 Cu 0.00025724 0.00029797 -0.00312095 + 125 3 Cu -0.00026362 0.00050680 -0.00216681 + 126 3 Cu 0.00115124 0.00002892 0.00062683 + 127 3 Cu 0.00188723 0.00080662 0.00001362 + 128 3 Cu 0.00101114 0.00002019 0.00023610 + 129 3 Cu 0.00047532 0.00017675 -0.00309748 + 130 3 Cu 0.00024262 -0.00054753 0.00150357 + 131 3 Cu 0.00010751 -0.00031021 0.00017243 + 132 3 Cu -0.00070183 -0.00037128 -0.00145492 + SUM OF ATOMIC FORCES 0.01051849 0.00856677 0.03641191 0.03885686 + + ******************************************************************************* + ENSEMBLE TYPE = NVT + STEP NUMBER = 1 + TIME [fs] = 0.500000 + CONSERVED QUANTITY [hartree] = -0.279168013085E+04 + + INSTANTANEOUS AVERAGES + CPU TIME [s] = 189.35 189.35 + ENERGY DRIFT PER ATOM [K] = 0.161227425822E+00 0.000000000000E+00 + POTENTIAL ENERGY[hartree] = -0.279186426278E+04 -0.279186426278E+04 + KINETIC ENERGY [hartree] = 0.183377348384E+00 0.183377348384E+00 + TEMPERATURE [K] = 294.687 294.687 + ******************************************************************************* + + + Spin 1 + + Number of electrons: 376 + Number of occupied orbitals: 380 + Number of molecular orbitals: 876 + + Spin 2 + + Number of electrons: 376 + Number of occupied orbitals: 380 + Number of molecular orbitals: 876 + + Number of orbital functions: 1844 + Number of independent orbital functions: 1844 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 Broy./Diag. 0.10E+00 3.7 0.02140482 -2791.8400586211 -2.79E+03 + 2 Broy./Diag. 0.10E+00 5.4 0.00058917 -2791.8597685538 -1.97E-02 + 3 Broy./Diag. 0.10E+00 5.4 0.00370547 -2791.8590630695 7.05E-04 + 4 Broy./Diag. 0.10E+00 5.4 0.00012260 -2791.8367456730 2.23E-02 + 5 Broy./Diag. 0.10E+00 5.4 0.00043467 -2791.8548546375 -1.81E-02 + 6 Broy./Diag. 0.10E+00 5.5 0.00012435 -2791.8744960079 -1.96E-02 + 7 Broy./Diag. 0.10E+00 5.5 0.00009025 -2791.8596582111 1.48E-02 + 8 Broy./Diag. 0.10E+00 5.5 0.00009115 -2791.8525148079 7.14E-03 + 9 Broy./Diag. 0.10E+00 5.5 0.00006751 -2791.8608135229 -8.30E-03 + 10 Broy./Diag. 0.10E+00 5.5 0.00008610 -2791.8622881969 -1.47E-03 + 11 Broy./Diag. 0.10E+00 5.5 0.00001237 -2791.8574516032 4.84E-03 + 12 Broy./Diag. 0.10E+00 5.5 0.00006419 -2791.8574356155 1.60E-05 + 13 Broy./Diag. 0.10E+00 5.5 0.00001160 -2791.8587761492 -1.34E-03 + 14 Broy./Diag. 0.10E+00 5.5 0.00004062 -2791.8572208644 1.56E-03 + 15 Broy./Diag. 0.10E+00 5.5 0.00001724 -2791.8548964617 2.32E-03 + 16 Broy./Diag. 0.10E+00 5.5 0.00001144 -2791.8558335614 -9.37E-04 + 17 Broy./Diag. 0.10E+00 5.5 0.00002007 -2791.8567085149 -8.75E-04 + 18 Broy./Diag. 0.10E+00 5.5 0.00001420 -2791.8570696854 -3.61E-04 + 19 Broy./Diag. 0.10E+00 5.5 0.00000658 -2791.8566746386 3.95E-04 + 20 Broy./Diag. 0.10E+00 5.5 0.00000380 -2791.8555632831 1.11E-03 + 21 Broy./Diag. 0.10E+00 5.5 0.00000933 -2791.8553949107 1.68E-04 + 22 Broy./Diag. 0.10E+00 5.5 0.00000314 -2791.8557319444 -3.37E-04 + 23 Broy./Diag. 0.10E+00 5.5 0.00000215 -2791.8561480687 -4.16E-04 + 24 Broy./Diag. 0.10E+00 5.5 0.00000413 -2791.8564768717 -3.29E-04 + 25 Broy./Diag. 0.10E+00 5.5 0.00000207 -2791.8565551743 -7.83E-05 + 26 Broy./Diag. 0.10E+00 5.5 0.00000156 -2791.8563379524 2.17E-04 + 27 Broy./Diag. 0.10E+00 5.5 0.00000079 -2791.8559318951 4.06E-04 + + *** SCF run converged in 27 steps *** + + + Electronic density on regular grids: -751.9999998352 0.0000001648 + Core density on regular grids: 751.9999999308 -0.0000000692 + Total charge density on r-space grids: 0.0000000956 + Total charge density g-space grids: 0.0000000956 + + Overlap energy of the core charge distribution: 0.00000145494520 + Self energy of the core charge distribution: -4333.05345429107729 + Core Hamiltonian energy: 1407.65783011926987 + Hartree energy: 624.19334833609173 + Exchange-correlation energy: -490.64949383909345 + Electronic entropic energy: -0.00416367284920 + Fermi energy: -0.00525396100347 + + Total energy: -2791.85593189508381 + + Integrated absolute spin density : 0.0000000000 + WARNING: S**2 computation does not yet treat fractional occupied orbitals + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -2791.856070742402608 + + + ATOMIC FORCES in [a.u.] + + # Atom Kind Element X Y Z + 1 1 H -0.00019239 0.00138268 0.00910702 + 2 1 H -0.00118770 0.00261965 -0.00003070 + 3 1 H -0.02453893 0.00095589 0.00527244 + 4 1 H -0.00254984 0.00650399 -0.00935049 + 5 1 H -0.00625445 0.00497017 -0.00569049 + 6 1 H 0.00274494 0.00311096 -0.00342557 + 7 1 H 0.00285935 0.01343493 0.00500962 + 8 1 H 0.00155548 -0.00300084 0.00148964 + 9 1 H 0.00855683 -0.00265058 0.00764542 + 10 1 H -0.00363250 -0.02246476 -0.00740521 + 11 1 H -0.00429608 0.01090386 -0.00458431 + 12 1 H 0.00546966 0.00222533 0.00523493 + 13 1 H 0.01133526 -0.00283577 -0.00824742 + 14 1 H -0.00827397 -0.01984602 -0.00160011 + 15 1 H -0.00238690 0.00433975 -0.00361898 + 16 1 H -0.00018777 0.00145485 -0.00395913 + 17 1 H 0.00345429 -0.00462037 -0.00366278 + 18 1 H -0.00342609 -0.00056295 -0.00026020 + 19 1 H 0.00704219 -0.00384490 -0.00480794 + 20 1 H -0.00043370 -0.00033087 -0.00219668 + 21 1 H 0.00115470 -0.00609653 0.00645413 + 22 1 H -0.00503266 0.00362817 0.00909417 + 23 1 H 0.02623615 -0.01608897 -0.01243257 + 24 1 H 0.00456750 -0.00387864 -0.00451041 + 25 1 H -0.02538669 -0.01466191 -0.00278913 + 26 1 H 0.00452354 0.00601522 0.00071407 + 27 1 H -0.00006053 -0.00059241 0.00462809 + 28 1 H 0.01131283 0.00758142 0.00196133 + 29 1 H 0.01509545 -0.01219245 0.00231899 + 30 1 H 0.00191116 -0.00084449 -0.00069425 + 31 1 H 0.00036249 -0.00910683 -0.00507711 + 32 1 H -0.00154599 0.00229103 -0.00559647 + 33 1 H -0.00297025 0.00115074 0.00607605 + 34 1 H -0.00246351 0.00047963 0.00731580 + 35 1 H 0.00212398 0.00132841 0.00074892 + 36 1 H 0.00997840 -0.01626142 -0.00229172 + 37 1 H -0.00316836 -0.00017472 -0.00255823 + 38 1 H -0.00241435 -0.00588603 -0.00282419 + 39 1 H 0.00736857 -0.00004910 -0.00933507 + 40 1 H 0.00767168 -0.00002260 0.01696732 + 41 1 H -0.00819394 0.01451270 0.00758405 + 42 1 H 0.00407896 -0.00377763 0.00377767 + 43 1 H -0.00729286 0.00612412 0.00132173 + 44 1 H 0.00876047 0.01982449 -0.00399746 + 45 1 H -0.00638192 0.00471835 0.00595852 + 46 1 H -0.01076831 -0.00847358 0.00034920 + 47 1 H -0.00203854 -0.01647165 -0.00690269 + 48 1 H 0.00713820 0.00323840 -0.00043055 + 49 1 H -0.00078137 0.00608276 0.00365072 + 50 1 H 0.00574649 0.00228533 -0.00293839 + 51 1 H 0.00088984 0.00939212 -0.01103204 + 52 1 H -0.02328684 -0.00653804 0.00135665 + 53 1 H -0.00430962 -0.00419681 0.00369557 + 54 1 H 0.02131788 0.01993666 0.01324356 + 55 1 H -0.00623865 0.01022967 -0.00983889 + 56 1 H 0.00188189 -0.01638079 -0.00382630 + 57 2 O 0.00297361 -0.00514840 -0.00106509 + 58 2 O -0.00356883 -0.00378648 0.00560186 + 59 2 O 0.01512845 0.00145721 -0.01886315 + 60 2 O 0.00086767 -0.01995346 0.00443920 + 61 2 O -0.00658133 0.02611943 0.02132226 + 62 2 O 0.00353387 -0.00829822 0.00704151 + 63 2 O -0.00937604 0.00606806 -0.00887727 + 64 2 O 0.00067898 -0.00116486 0.01269750 + 65 2 O 0.01188400 0.02138013 0.00296979 + 66 2 O -0.00536283 0.00314759 0.00169179 + 67 2 O -0.00109393 -0.00217659 -0.00653983 + 68 2 O -0.02339955 0.01532630 0.00621666 + 69 2 O -0.00667991 -0.00639395 -0.00752434 + 70 2 O 0.00677829 -0.00528790 -0.00784967 + 71 2 O 0.02031290 0.01831550 0.01059574 + 72 2 O -0.02580981 0.00389220 -0.00453046 + 73 2 O 0.00216709 0.00836162 0.00717658 + 74 2 O -0.01562830 0.01574107 0.01528848 + 75 2 O 0.00234843 0.01085456 -0.00074157 + 76 2 O 0.00101456 0.00771072 -0.01565871 + 77 2 O 0.00526623 0.00175332 0.00264626 + 78 2 O -0.00250751 -0.02556638 0.00398811 + 79 2 O -0.00396895 0.01100291 -0.01329931 + 80 2 O 0.01057951 -0.02752346 0.00434703 + 81 2 O 0.00436733 -0.00812711 -0.00506630 + 82 2 O 0.01600772 0.02476575 0.00727209 + 83 2 O -0.00765833 -0.01626642 -0.01277964 + 84 2 O -0.00271561 -0.01482080 0.01072771 + 85 3 Cu 0.00009637 0.00018711 -0.00013586 + 86 3 Cu -0.00014256 0.00078755 -0.00257085 + 87 3 Cu 0.00037717 -0.00025931 -0.00146915 + 88 3 Cu 0.00077314 0.00041209 0.00050245 + 89 3 Cu -0.00009259 0.00035482 -0.00207806 + 90 3 Cu -0.00034629 0.00015505 -0.00147268 + 91 3 Cu 0.00004928 -0.00014385 -0.00197053 + 92 3 Cu -0.00035481 0.00024325 -0.00057167 + 93 3 Cu -0.00021937 0.00037292 -0.00170667 + 94 3 Cu -0.00035343 0.00021389 -0.00093475 + 95 3 Cu -0.00015925 0.00003673 -0.00019779 + 96 3 Cu 0.00036410 0.00007040 -0.00180713 + 97 3 Cu -0.00000706 0.00028795 -0.00095439 + 98 3 Cu -0.00004292 -0.00009356 -0.00166586 + 99 3 Cu -0.00033223 -0.00052564 -0.00210577 + 100 3 Cu -0.00044034 -0.00037536 -0.00170560 + 101 3 Cu -0.00011368 0.00081691 0.00294252 + 102 3 Cu 0.00141590 0.00087735 0.00225210 + 103 3 Cu -0.00097167 0.00234222 0.00326419 + 104 3 Cu 0.00099386 0.00213780 0.00302065 + 105 3 Cu 0.00109683 0.00098711 0.00390896 + 106 3 Cu 0.00094641 -0.00071533 0.00504375 + 107 3 Cu 0.00010243 -0.00018897 0.00229013 + 108 3 Cu -0.00048036 0.00085715 0.00264886 + 109 3 Cu 0.00250568 -0.00114376 0.00712742 + 110 3 Cu -0.00057774 0.00082289 0.00504162 + 111 3 Cu 0.00102360 0.00272340 0.00389079 + 112 3 Cu -0.00061461 -0.00036516 0.00265580 + 113 3 Cu 0.00029341 -0.00058324 0.00459409 + 114 3 Cu -0.00113608 -0.00000531 0.00557048 + 115 3 Cu -0.00006507 0.00071262 0.00267218 + 116 3 Cu 0.00073731 -0.00003023 0.00256045 + 117 3 Cu -0.00142172 -0.00004212 0.00014643 + 118 3 Cu 0.00057127 -0.00209679 -0.00048770 + 119 3 Cu -0.00092327 0.00049833 -0.00345012 + 120 3 Cu -0.00051262 0.00105170 0.00132778 + 121 3 Cu -0.00025188 -0.00090955 0.00101099 + 122 3 Cu -0.00006300 0.00070922 -0.00246754 + 123 3 Cu -0.00015248 -0.00162829 0.00432645 + 124 3 Cu 0.00059684 0.00010246 -0.00287864 + 125 3 Cu -0.00061769 0.00074702 -0.00203577 + 126 3 Cu 0.00161071 0.00066957 0.00035313 + 127 3 Cu 0.00183602 0.00100328 -0.00003308 + 128 3 Cu 0.00077514 0.00037686 0.00018102 + 129 3 Cu 0.00061373 0.00053219 -0.00312697 + 130 3 Cu 0.00070194 -0.00119116 0.00145384 + 131 3 Cu 0.00013129 -0.00017470 0.00002850 + 132 3 Cu -0.00135067 -0.00069093 -0.00138632 + SUM OF ATOMIC FORCES 0.01087024 0.01017860 0.03788899 0.04071046 + + ******************************************************************************* + ENSEMBLE TYPE = NVT + STEP NUMBER = 2 + TIME [fs] = 1.000000 + CONSERVED QUANTITY [hartree] = -0.279167993512E+04 + + INSTANTANEOUS AVERAGES + CPU TIME [s] = 157.11 173.23 + ENERGY DRIFT PER ATOM [K] = 0.629459527986E+00 0.314729763993E+00 + POTENTIAL ENERGY[hartree] = -0.279185607074E+04 -0.279186016676E+04 + KINETIC ENERGY [hartree] = 0.175111784068E+00 0.179244566226E+00 + TEMPERATURE [K] = 281.404 288.045 + ******************************************************************************* + + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER TOTAL BLAS SMM ACC + flops 5 x 12 x 5 15052800 100.0% 0.0% 0.0% + flops 13 x 12 x 5 19568640 100.0% 0.0% 0.0% + flops 5 x 12 x 13 19568640 100.0% 0.0% 0.0% + flops 13 x 12 x 13 25309440 100.0% 0.0% 0.0% + flops 25 x 12 x 5 64512000 100.0% 0.0% 0.0% + flops 5 x 12 x 25 64512000 100.0% 0.0% 0.0% + flops 13 x 12 x 25 83304000 100.0% 0.0% 0.0% + flops 25 x 12 x 13 83304000 100.0% 0.0% 0.0% + flops 25 x 12 x 25 276480000 100.0% 0.0% 0.0% + flops 5 x 5 x 76 776294400 100.0% 0.0% 0.0% + flops 13 x 5 x 76 991477760 100.0% 0.0% 0.0% + flops 5 x 13 x 76 991477760 100.0% 0.0% 0.0% + flops 5 x 32 x 5 1083801600 100.0% 0.0% 0.0% + flops 13 x 13 x 76 1328377856 100.0% 0.0% 0.0% + flops 13 x 32 x 5 1408942080 100.0% 0.0% 0.0% + flops 5 x 32 x 13 1408942080 100.0% 0.0% 0.0% + flops 13 x 32 x 13 1822279680 100.0% 0.0% 0.0% + flops 5 x 5 x 96 2941747200 100.0% 0.0% 0.0% + flops 25 x 5 x 76 3268608000 100.0% 0.0% 0.0% + flops 5 x 25 x 76 3268608000 100.0% 0.0% 0.0% + flops 13 x 5 x 96 3757178880 100.0% 0.0% 0.0% + flops 5 x 13 x 96 3757178880 100.0% 0.0% 0.0% + flops 13 x 25 x 76 4198604800 100.0% 0.0% 0.0% + flops 25 x 13 x 76 4242867200 100.0% 0.0% 0.0% + flops 25 x 32 x 5 4644864000 100.0% 0.0% 0.0% + flops 5 x 32 x 25 4644864000 100.0% 0.0% 0.0% + flops 13 x 13 x 96 5033852928 100.0% 0.0% 0.0% + flops 5 x 5 x 64 5229772800 100.0% 0.0% 0.0% + flops 13 x 32 x 25 5997888000 100.0% 0.0% 0.0% + flops 25 x 32 x 13 5997888000 100.0% 0.0% 0.0% + flops 13 x 5 x 64 6679429120 100.0% 0.0% 0.0% + flops 5 x 13 x 64 6679429120 100.0% 0.0% 0.0% + flops 13 x 13 x 64 8949071872 100.0% 0.0% 0.0% + flops 25 x 5 x 96 12386304000 100.0% 0.0% 0.0% + flops 5 x 25 x 96 12386304000 100.0% 0.0% 0.0% + flops 25 x 25 x 76 14300160000 100.0% 0.0% 0.0% + flops 13 x 25 x 96 15910502400 100.0% 0.0% 0.0% + flops 25 x 13 x 96 16078233600 100.0% 0.0% 0.0% + flops 25 x 32 x 25 19906560000 100.0% 0.0% 0.0% + flops 25 x 5 x 64 22020096000 100.0% 0.0% 0.0% + flops 5 x 25 x 64 22020096000 100.0% 0.0% 0.0% + flops 13 x 25 x 64 28285337600 100.0% 0.0% 0.0% + flops 25 x 13 x 64 28583526400 100.0% 0.0% 0.0% + flops 25 x 25 x 96 54190080000 100.0% 0.0% 0.0% + flops 25 x 25 x 64 96337920000 100.0% 0.0% 0.0% + flops inhomo. stacks 0 0.0% 0.0% 0.0% + flops total 432.160178E+09 100.0% 0.0% 0.0% + flops max/rank 19.042264E+09 100.0% 0.0% 0.0% + matmuls inhomo. stacks 0 0.0% 0.0% 0.0% + matmuls total 17364160 100.0% 0.0% 0.0% + number of processed stacks 355968 100.0% 0.0% 0.0% + average stack size 48.8 0.0 0.0 + marketing flops 378.444186E+09 + ------------------------------------------------------------------------------- + # multiplications 136 + max memory usage/rank 348.073984E+06 + # max total images/rank 3 + # max 3D layers 1 + # MPI messages exchanged 81600 + MPI messages size (bytes): + total size 18.144055E+09 + min size 149.504000E+03 + max size 608.792000E+03 + average size 222.353625E+03 + MPI breakdown and total messages size (bytes): + size <= 128 0 0 + 128 < size <= 8192 0 0 + 8192 < size <= 32768 0 0 + 32768 < size <= 131072 0 0 + 131072 < size <= 4194304 81600 18144051840 + 4194304 < size <= 16777216 0 0 + 16777216 < size 0 0 + ------------------------------------------------------------------------------- + + *** WARNING in dbcsr/mm/dbcsr_mm.F:268 :: Using a non-square number of *** + *** MPI ranks might lead to poor performance. *** + *** Used ranks: 24 *** + *** Suggested: 25 49 *** + + ------------------------------------------------------------------------------- + + MEMORY| Estimated peak process memory [MiB] 333 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 132 + MP_Bcast 2188 264034. + MP_Allreduce 2303 380. + MP_Sync 10 + MP_Alltoall 6065 2879679. + MP_ISendRecv 11224 33984. + MP_Wait 37456 + MP_comm_split 6 + MP_ISend 23452 136936. + MP_IRecv 23212 137457. + MP_Recv 260 472064. + MP_Memory 26008 + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 6.1, the CP2K developers group (2018). + CP2K is freely available from https://www.cp2k.org/ . + + Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost. + Electronic Structure Calculations on Graphics Processing Units, John Wiley & Sons, Ltd, 173-190 (2016). + GPU-Accelerated Sparse Matrix-Matrix Multiplication for Linear Scaling Density Functional Theory. + http://dx.doi.org/10.1002/9781118670712.ch8 + + + Borstnik, U; VandeVondele, J; Weber, V; Hutter, J. + PARALLEL COMPUTING, 40 (5-6), 47-58 (2014). + Sparse matrix multiplication: The distributed block-compressed sparse + row library. + http://dx.doi.org/10.1016/j.parco.2014.03.012 + + + Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J. + WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 4 (1), 15-25 (2014). + CP2K: atomistic simulations of condensed matter systems. + http://dx.doi.org/10.1002/wcms.1159 + + + VandeVondele, J; Hutter, J. + JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007). + Gaussian basis sets for accurate calculations on molecular systems in + gas and condensed phases. + http://dx.doi.org/10.1063/1.2770708 + + + Krack, M. + THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005). + Pseudopotentials for H to Kr optimized for gradient-corrected + exchange-correlation functionals. + http://dx.doi.org/10.1007/s00214-005-0655-y + + + VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T; + Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005). + QUICKSTEP: Fast and accurate density functional calculations using a + mixed Gaussian and plane waves approach. + http://dx.doi.org/10.1016/j.cpc.2004.12.014 + + + Frigo, M; Johnson, SG. + PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005). + The design and implementation of FFTW3. + http://dx.doi.org/10.1109/JPROC.2004.840301 + + + Kolafa, J. + JOURNAL OF COMPUTATIONAL CHEMISTRY, 25 (3), 335-342 (2004). + Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules. + http://dx.doi.org/10.1002/jcc.10385 + + + Hartwigsen, C; Goedecker, S; Hutter, J. + PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998). + Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. + http://dx.doi.org/10.1103/PhysRevB.58.3641 + + + Lippert, G; Hutter, J; Parrinello, M. + MOLECULAR PHYSICS, 92 (3), 477-487 (1997). + A hybrid Gaussian and plane wave density functional scheme. + http://dx.doi.org/10.1080/002689797170220 + + + Perdew, JP; Burke, K; Ernzerhof, M. + PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996). + Generalized gradient approximation made simple. + http://dx.doi.org/10.1103/PhysRevLett.77.3865 + + + Goedecker, S; Teter, M; Hutter, J. + PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996). + Separable dual-space Gaussian pseudopotentials. + http://dx.doi.org/10.1103/PhysRevB.54.1703 + + + NOSE, S. JOURNAL OF CHEMICAL PHYSICS, 81 (1), 511-519 (1984). + A UNIFIED FORMULATION OF THE CONSTANT TEMPERATURE MOLECULAR-DYNAMICS + METHODS. + http://dx.doi.org/10.1063/1.447334 + + + NOSE, S. MOLECULAR PHYSICS, 52 (2), 255-268 (1984). + A MOLECULAR-DYNAMICS METHOD FOR SIMULATIONS IN THE CANONICAL ENSEMBLE. + http://dx.doi.org/10.1080/00268978400101201 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.010 0.012 346.712 346.713 + qs_mol_dyn_low 1 2.0 0.003 0.004 346.469 346.472 + qs_forces 3 3.7 0.001 0.001 346.445 346.445 + qs_energies 3 4.7 0.000 0.000 329.649 329.652 + scf_env_do_scf 3 5.7 0.000 0.000 320.907 321.094 + scf_env_do_scf_inner_loop 58 6.9 0.005 0.007 320.892 321.079 + velocity_verlet 2 3.0 0.001 0.001 315.565 315.565 + rebuild_ks_matrix 61 8.8 0.000 0.000 166.198 166.209 + qs_ks_build_kohn_sham_matrix 61 9.8 0.010 0.012 166.198 166.209 + qs_ks_update_qs_env 58 7.9 0.001 0.001 155.822 155.845 + sum_up_and_integrate 61 10.8 0.258 0.299 135.085 135.105 + integrate_v_rspace 122 11.8 93.562 126.932 134.826 134.888 + qs_rho_update_rho 61 8.0 0.001 0.001 99.394 99.411 + calculate_rho_elec 122 9.0 67.490 89.581 99.393 99.410 + qs_scf_new_mos 58 7.9 0.003 0.005 59.723 59.766 + eigensolver 116 8.9 0.008 0.013 55.707 55.746 + mp_alltoall_d11v 1807 12.2 34.105 54.016 34.105 54.016 + rs_distribute_matrix 250 11.3 0.394 0.523 34.462 53.954 + density_rs2pw 122 10.0 0.007 0.008 30.151 45.664 + cp_fm_syevd 122 10.0 0.001 0.001 43.991 44.140 + cp_fm_syevd_base 122 11.0 43.800 44.115 43.800 44.115 + rs_pw_transfer 982 12.3 0.009 0.010 27.942 43.413 + mp_waitany 15308 14.3 23.710 39.400 23.710 39.400 + rs_pw_transfer_RS2PW_180 125 11.9 0.707 0.800 23.450 39.006 + pw_transfer 2248 12.4 0.169 0.228 32.758 34.115 + fft_wrap_pw1pw2 2126 13.4 0.022 0.030 32.402 33.801 + fft_wrap_pw1pw2_180 1394 14.4 2.961 3.593 31.212 32.680 + qs_vxc_create 61 10.8 0.002 0.002 28.666 28.761 + xc_vxc_pw_create 61 11.8 0.897 1.032 28.665 28.760 + fft3d_ps 2126 15.4 14.143 16.005 23.326 27.441 + xc_rho_set_and_dset_create 61 12.8 0.421 0.455 14.720 14.785 + mp_alltoall_z22v 2126 17.4 6.057 12.057 6.057 12.057 + cp_fm_triangular_multiply 348 9.9 11.769 11.896 11.769 11.896 + gspace_mixing 55 7.9 0.131 0.134 10.494 10.494 + qs_ks_update_qs_env_forces 3 4.7 0.000 0.000 10.459 10.460 + x_to_yz 1147 16.7 1.813 2.067 5.103 8.326 + potential_pw2rs 122 12.8 0.021 0.022 7.372 7.441 + broyden_mixing 55 8.9 6.371 7.103 7.225 7.287 + ------------------------------------------------------------------------------- + + The number of warnings for this run is : 1 + + ------------------------------------------------------------------------------- + **** **** ****** ** PROGRAM ENDED AT 2019-12-21 14:12:30.188 + ***** ** *** *** ** PROGRAM RAN ON node16 + ** **** ****** PROGRAM RAN BY nxu + ***** ** ** ** ** PROGRAM PROCESS ID 287845 + **** ** ******* ** PROGRAM STOPPED IN /public/home/apclab/nxu/uk/cu100-h2o- + aimd-test_force diff --git a/tests/cp2k/aimd/cp2k.pbs b/tests/cp2k/aimd/cp2k.pbs new file mode 100644 index 000000000..a5b05efa3 --- /dev/null +++ b/tests/cp2k/aimd/cp2k.pbs @@ -0,0 +1,17 @@ +#/bin/bash +#PBS -N cp2k +#PBS -q batch +#PBS -l nodes=1:ppn=24 +#PBS -j oe +#PBS -l walltime=1000:0:0 + +JOB=cp2k.inp +JOBNAME=`basename "$JOB" .inp` + +nprocs=`cat $PBS_NODEFILE | wc -l` +source /public/software/profile.d/cp2k.sh + +cd $PBS_O_WORKDIR +mpirun -np $nprocs -machinefile $PBS_NODEFILE /public/source/cp2k-6.1.0/exe/Linux-x86-64-intel/cp2k.popt -i $JOB -o "$JOBNAME.log" + + diff --git a/tests/cp2k/aimd/deepmd/box.raw b/tests/cp2k/aimd/deepmd/box.raw new file mode 100644 index 000000000..b63a7234e --- /dev/null +++ b/tests/cp2k/aimd/deepmd/box.raw @@ -0,0 +1,3 @@ +1.024248981475830078e+01 0.000000000000000000e+00 0.000000000000000000e+00 6.271716226903761935e-16 1.024248981475830078e+01 0.000000000000000000e+00 1.408343787828714427e-15 1.408343787828714427e-15 2.300000000000000000e+01 +1.024248981475830078e+01 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6.19398943 + 0.43330514 0.80046604 10.23399572 + 0.06330514 4.01991233 2.15398314 + 0.31330514 4.38991233 6.19398943 + 0.56330514 4.75991233 10.23399572 + 1.99074314 -0.08643496 0.06633974 + 2.24074314 0.28356504 4.10634603 + 2.49074314 0.65356504 8.14635232 + 2.12074314 3.87301133 0.06633974 + 2.37074314 4.24301133 4.10634603 + 2.62074314 4.61301133 8.14635232 + 0.08855984 2.07830314 0.06225474 + 0.33855984 2.44830314 4.10226103 + 0.58855984 2.81830314 8.14226732 + 0.21855984 6.03774943 0.06225474 + 0.46855984 6.40774943 4.10226103 + 0.71855984 6.77774943 8.14226732 + 2.03247314 2.02170314 2.02538314 + 2.28247314 2.39170314 6.06538943 + 2.53247314 2.76170314 10.10539572 + 2.16247314 5.98114943 2.02538314 + 2.41247314 6.35114943 6.06538943 + 2.66247314 6.72114943 10.10539572 + -0.04486496 0.11535714 0.05402634 + 0.20513504 0.48535714 4.09403263 + 0.45513504 0.85535714 8.13403892 + 0.08513504 4.07480343 0.05402634 + 0.33513504 4.44480343 4.09403263 + 0.58513504 4.81480343 8.13403892 + 1.96647314 1.93138314 -0.14058486 + 2.21647314 2.30138314 3.89942143 + 2.46647314 2.67138314 7.93942772 + 2.09647314 5.89082943 -0.14058486 + 2.34647314 6.26082943 3.89942143 + 2.59647314 6.63082943 7.93942772 + 2.08077314 0.00650580 1.99560314 + 2.33077314 0.37650580 6.03560943 + 2.58077314 0.74650580 10.07561572 + 2.21077314 3.96595209 1.99560314 + 2.46077314 4.33595209 6.03560943 + 2.71077314 4.70595209 10.07561572 + 0.06321854 1.99994314 2.04389314 + 0.31321854 2.36994314 6.08389943 + 0.56321854 2.73994314 10.12390572 + 0.19321854 5.95938943 2.04389314 + 0.44321854 6.32938943 6.08389943 + 0.69321854 6.69938943 10.12390572 diff --git a/tests/poscars/POSCAR.SiC.uniform b/tests/poscars/POSCAR.SiC.uniform new file mode 100644 index 000000000..9a6214267 --- /dev/null +++ b/tests/poscars/POSCAR.SiC.uniform @@ -0,0 +1,16 @@ +C4 Si4 +1.0 +4.0817852422279959e+00 -8.0334347485565818e-20 1.4195449766884313e-17 +1.2315711101650186e-01 3.7860044730134366e+00 -1.7522489439993958e-18 +4.0639226354941010e-01 3.2444019947671882e-01 4.2124083393682454e+00 +C Si +4 4 +Cartesian + -0.1022885809 0.5553879154 2.3401729917 + 1.4574918226 -0.0391762715 0.0190932943 + -0.0904993945 1.7684440711 -0.1710987880 + 2.0638159391 2.1681985074 2.4580083474 + -0.3261354126 0.1759255681 0.2236316249 + 2.0738703301 2.3024191125 -0.5031567813 + 2.3488610334 0.3825072268 1.7330866249 + -0.0534780340 1.5938442575 1.8486892947 diff --git a/tests/test_cell_to_low_triangle.py b/tests/test_cell_to_low_triangle.py new file mode 100644 index 000000000..ca60b35d1 --- /dev/null +++ b/tests/test_cell_to_low_triangle.py @@ -0,0 +1,49 @@ +import os +import numpy as np +import unittest +from context import dpdata + +class TestCellToLowTriangle(unittest.TestCase): + def test_func1(self): + cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(6,6,6,np.pi*1/2, np.pi*1/2, np.pi*1/2) + cell_2 = np.asarray([[6,0,0],[0,6,0],[0,0,6]]) + for ii in range(3): + for jj in range(3): + self.assertAlmostEqual(cell_1[ii,jj], cell_2[ii,jj], places=6) + + def test_func2(self): + cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(6,6,6,np.pi*1/3, np.pi*1/3, np.pi*1/3) + cell_2 = np.asarray([ + [6,0,0], + [3,3*np.sqrt(3),0], + [3,np.sqrt(3),2*np.sqrt(6)]]) + for ii in range(3): + for jj in range(3): + self.assertAlmostEqual(cell_1[ii,jj], cell_2[ii,jj], places=6) + + def test_func3(self): + cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(6,7,8,np.pi*133/180,np.pi*84/180,np.pi*69/180) + cell_2 = np.asarray([[ 6.0, 0.0, 0.0], + [ 2.5085757, 6.535063 , 0.0], + [ 0.8362277, -6.1651506, 5.0290794]], dtype='float32') + for ii in range(3): + for jj in range(3): + self.assertAlmostEqual(cell_1[ii,jj], cell_2[ii,jj], places=6) + + def test_func4(self): + with self.assertRaises(Exception) as c: + dpdata.cp2k.cell.cell_to_low_triangle(0.1,6,6,np.pi*1/2,np.pi*1/2,np.pi*1/2) + self.assertTrue("A==0.1" in str(c.exception)) + + def test_func5(self): + with self.assertRaises(Exception) as c: + dpdata.cp2k.cell.cell_to_low_triangle(6,6,6,np.pi*3/180,np.pi*1/2,np.pi*1/2) + self.assertTrue("alpha" in str(c.exception)) + + def test_func6(self): + with self.assertRaises(Exception) as c: + dpdata.cp2k.cell.cell_to_low_triangle(6,7,8,np.pi*153/180,np.pi*84/180,np.pi*69/180) + self.assertTrue("lz^2" in str(c.exception)) + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_cp2k_aimd_output.py b/tests/test_cp2k_aimd_output.py new file mode 100644 index 000000000..3eb0ce789 --- /dev/null +++ b/tests/test_cp2k_aimd_output.py @@ -0,0 +1,17 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompLabeledSys + +class TestCp2kAimdOutput(unittest.TestCase, CompLabeledSys): + def setUp (self) : + self.system_1 = dpdata.LabeledSystem('cp2k/aimd',fmt='cp2k/aimd_output') + self.system_2 = dpdata.LabeledSystem('cp2k/aimd/deepmd', fmt='deepmd/raw') + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 4 + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_deepmd_comp.py b/tests/test_deepmd_comp.py index 0536d3248..840712af4 100644 --- a/tests/test_deepmd_comp.py +++ b/tests/test_deepmd_comp.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys, CompSys +from comp_sys import CompLabeledSys, CompSys, IsPBC -class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys): +class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') @@ -25,7 +25,7 @@ def tearDown(self) : shutil.rmtree('tmp.deepmd.npy') -class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) : +class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) : def setUp (self) : self.system_1 = dpdata.System('poscars/POSCAR.h2o.md', fmt = 'vasp/poscar') @@ -45,7 +45,7 @@ def tearDown(self) : shutil.rmtree('tmp.deepmd.npy') -class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) : +class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) : def setUp(self) : self.dir_name = 'tmp.deepmd.npy.nol' natoms = 3 diff --git a/tests/test_deepmd_raw.py b/tests/test_deepmd_raw.py index 7778371e3..241da7167 100644 --- a/tests/test_deepmd_raw.py +++ b/tests/test_deepmd_raw.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys, CompSys +from comp_sys import CompLabeledSys, CompSys, IsPBC -class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys): +class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') @@ -17,7 +17,7 @@ def setUp (self) : self.v_places = 6 -class TestDeepmdDumpRaw(unittest.TestCase, CompLabeledSys): +class TestDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') @@ -131,7 +131,7 @@ def test_npy_type_map_enforce (self) : -class TestDeepmdRawNoLabels(unittest.TestCase, CompSys) : +class TestDeepmdRawNoLabels(unittest.TestCase, CompSys, IsPBC) : def setUp (self) : self.system_1 = dpdata.System('poscars/POSCAR.h2o.md', fmt = 'vasp/poscar') @@ -149,7 +149,7 @@ def tearDown(self) : shutil.rmtree('tmp.deepmd') -class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) : +class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) : def setUp(self) : self.dir_name = 'tmp.deepmd.nol' natoms = 3 diff --git a/tests/test_gaussian_log.py b/tests/test_gaussian_log.py index df576fb40..039c1d6c8 100644 --- a/tests/test_gaussian_log.py +++ b/tests/test_gaussian_log.py @@ -2,7 +2,6 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys class TestGaussianLog : def test_atom_names(self) : @@ -18,6 +17,9 @@ def test_atom_types(self) : for ii in range(len(self.atom_types)) : self.assertEqual(self.system.data['atom_types'][ii], self.atom_types[ii]) + def test_nopbc(self): + self.assertEqual(self.system.nopbc, True) + class TestGaussianLoadLog(unittest.TestCase, TestGaussianLog): def setUp (self) : self.system = dpdata.LabeledSystem('gaussian/methane.gaussianlog', diff --git a/tests/test_json.py b/tests/test_json.py index 15f7e0117..98be14040 100644 --- a/tests/test_json.py +++ b/tests/test_json.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys +from comp_sys import CompLabeledSys, IsPBC -class TestJsonLoad(unittest.TestCase, CompLabeledSys): +class TestJsonLoad(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') @@ -14,7 +14,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestAsDict(unittest.TestCase, CompLabeledSys): +class TestAsDict(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') diff --git a/tests/test_lammps_dump_skipload.py b/tests/test_lammps_dump_skipload.py index 9ec7ade62..9e6502f61 100644 --- a/tests/test_lammps_dump_skipload.py +++ b/tests/test_lammps_dump_skipload.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompSys +from comp_sys import CompSys, IsPBC -class TestLmpDumpSkip(unittest.TestCase, CompSys): +class TestLmpDumpSkip(unittest.TestCase, CompSys, IsPBC): def setUp(self): self.system_1 = dpdata.System(os.path.join('poscars', 'conf.5.dump'), diff --git a/tests/test_multisystems.py b/tests/test_multisystems.py index 2d8606626..8bf285dcc 100644 --- a/tests/test_multisystems.py +++ b/tests/test_multisystems.py @@ -4,6 +4,7 @@ from context import dpdata from comp_sys import CompSys from comp_sys import CompLabeledSys +from comp_sys import IsNoPBC from itertools import permutations class MultiSystems: @@ -17,7 +18,7 @@ def test_systems_size(self): def test_atom_names(self): self.assertEqual(self.atom_names, self.systems.atom_names) -class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems): +class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC): def setUp(self): self.places = 6 self.e_places = 6 @@ -39,7 +40,7 @@ def setUp(self): self.atom_names = ['C', 'H'] -class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems): +class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC): def setUp(self): self.places = 6 self.e_places = 6 @@ -76,7 +77,7 @@ def setUp(self): self.system_sizes = {'C1H4O0':1, 'C0H0O2':1} self.atom_names = ['C', 'H', 'O'] -class TestMultiDeepmdDumpRaw(unittest.TestCase, CompLabeledSys): +class TestMultiDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsNoPBC): def setUp (self) : self.places = 6 self.e_places = 6 @@ -94,7 +95,7 @@ def setUp (self) : self.system_1 = dpdata.LabeledSystem(os.path.join(path, 'C1H3'), fmt='deepmd/raw', type_map = ['C', 'H']) self.system_2 = system_3 -class TestMultiDeepmdDumpComp(unittest.TestCase, CompLabeledSys): +class TestMultiDeepmdDumpComp(unittest.TestCase, CompLabeledSys, IsNoPBC): def setUp (self) : self.places = 6 self.e_places = 4 diff --git a/tests/test_perturb.py b/tests/test_perturb.py new file mode 100644 index 000000000..fe63882f0 --- /dev/null +++ b/tests/test_perturb.py @@ -0,0 +1,137 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompSys, IsPBC + +from unittest.mock import Mock +from unittest.mock import patch, MagicMock + +class NormalGenerator(object): + def __init__(self): + self.randn_generator = self.get_randn_generator() + self.rand_generator = self.get_rand_generator() + def randn(self,number): + return next(self.randn_generator) + def rand(self,number): + return next(self.rand_generator) + @staticmethod + def get_randn_generator(): + data = np.asarray([ + [ 0.71878148, -2.20667426, 1.49373955], + [-0.42728113, 1.43836059, -1.17553854], + [-1.70793073, -0.39588759, -0.40880927], + [ 0.17078291, -0.34856352, 1.04307936], + [-0.99103413, -0.1886479, 0.13813131], + [ 0.5839343, 1.04612646, -0.62631026], + [ 0.9752889, 1.85932517, -0.47875828], + [-0.23977172, -0.38373444, -0.04375488]]) + count = 0 + while True: + yield data[count] + count +=1 + + @staticmethod + def get_rand_generator(): + yield np.asarray([0.23182233, 0.87106847, 0.68728511, 0.94180274, 0.92860453, 0.69191187]) + +class UniformGenerator(object): + def __init__(self): + self.randn_generator = self.get_randn_generator() + self.rand_generator = self.get_rand_generator() + def randn(self,number): + return next(self.randn_generator) + def rand(self,number): + return next(self.rand_generator) + + @staticmethod + def get_randn_generator(): + data = [[-0.19313281, 0.80194715, 0.14050915], + [-1.47859926, 0.12921667, -0.17632456], + [-0.60836805, -0.7700423, -0.8386948 ], + [-0.03236753, 0.36690245, 0.5041072 ], + [-1.59366933, 0.37069227, 0.89608291], + [ 0.18165617, 0.53875315, -0.42233955], + [ 0.74052496, 1.26627555, -1.12094823], + [-0.89610092, -1.44247021, -1.3502529 ]] + yield np.asarray([0.0001,0.0001,0.0001]) # test for not using small vector + count = 0 + while True: + yield data[count] + count +=1 + + @staticmethod + def get_rand_generator(): + data = np.asarray([[0.71263084], [0.61339295], + [0.22948181], [0.36087632], + [0.17582222], [0.97926742], + [0.84706761], [0.44495513]]) + + yield np.asarray([0.34453551, 0.0618966, 0.9327273, 0.43013654, 0.88624993, 0.48827425]) + count =0 + while True: + yield np.asarray(data[count]) + count+=1 + +class ConstGenerator(object): + def __init__(self): + self.randn_generator = self.get_randn_generator() + self.rand_generator = self.get_rand_generator() + def randn(self,number): + return next(self.randn_generator) + def rand(self,number): + return next(self.rand_generator) + + @staticmethod + def get_randn_generator(): + data = np.asarray([[ 0.95410606, -1.62338002, -2.05359934], + [ 0.69213769, -1.26008667, 0.77970721], + [-1.77926476, -0.39227219, 2.31677298], + [ 0.08785233, -0.03966649, -0.45325656], + [-0.53860887, 0.42536802, -0.46167309], + [-0.26865791, -0.19901684, -2.51444768], + [-0.31627314, 0.22076982, -0.36032225], + [0.66731887, 1.2505806, 1.46112938]]) + yield np.asarray([0.0001,0.0001,0.0001]) # test for not using small vector + count = 0 + while True: + yield data[count] + count +=1 + + @staticmethod + def get_rand_generator(): + yield np.asarray([0.01525907, 0.68387374, 0.39768541, 0.55596047, 0.26557088, 0.60883073]) + +# %% +class TestPerturbNormal(unittest.TestCase, CompSys, IsPBC): + @patch('numpy.random') + def setUp (self, random_mock): + random_mock.rand = NormalGenerator().rand + random_mock.randn = NormalGenerator().randn + system_1_origin = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.system_1 = system_1_origin.perturb(1,0.05,0.6,'normal') + self.system_2 = dpdata.System('poscars/POSCAR.SiC.normal',fmt='vasp/poscar') + self.places = 6 + +class TestPerturbUniform(unittest.TestCase, CompSys, IsPBC): + @patch('numpy.random') + def setUp (self, random_mock) : + random_mock.rand = UniformGenerator().rand + random_mock.randn = UniformGenerator().randn + system_1_origin = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.system_1 = system_1_origin.perturb(1,0.05,0.6,'uniform') + self.system_2 = dpdata.System('poscars/POSCAR.SiC.uniform',fmt='vasp/poscar') + self.places = 6 + +class TestPerturbConst(unittest.TestCase, CompSys, IsPBC): + @patch('numpy.random') + def setUp (self, random_mock) : + random_mock.rand = ConstGenerator().rand + random_mock.randn = ConstGenerator().randn + system_1_origin = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.system_1 = system_1_origin.perturb(1,0.05,0.6,'const') + self.system_2 = dpdata.System('poscars/POSCAR.SiC.const',fmt='vasp/poscar') + self.places = 6 + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/tests/test_qe_cp_traj_skipload.py b/tests/test_qe_cp_traj_skipload.py index 1e1b31f88..dc02e6323 100644 --- a/tests/test_qe_cp_traj_skipload.py +++ b/tests/test_qe_cp_traj_skipload.py @@ -4,8 +4,9 @@ from context import dpdata from comp_sys import CompSys from comp_sys import CompLabeledSys +from comp_sys import IsPBC -class TestPWSCFTrajSkip(unittest.TestCase, CompSys): +class TestPWSCFTrajSkip(unittest.TestCase, CompSys, IsPBC): def setUp(self): self.system_1 = dpdata.System(os.path.join('qe.traj', 'traj6'), fmt = 'qe/cp/traj', @@ -21,7 +22,7 @@ def setUp(self): self.f_places = 6 self.v_places = 4 -class TestPWSCFLabeledTrajSkip(unittest.TestCase, CompLabeledSys): +class TestPWSCFLabeledTrajSkip(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): self.system_1 = dpdata.LabeledSystem(os.path.join('qe.traj', 'traj6'), fmt = 'qe/cp/traj', diff --git a/tests/test_quip_gap_xyz.py b/tests/test_quip_gap_xyz.py index 20d40b2f3..abfabb627 100644 --- a/tests/test_quip_gap_xyz.py +++ b/tests/test_quip_gap_xyz.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys +from comp_sys import CompLabeledSys, IsPBC -class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.multi_systems = dpdata.MultiSystems.from_file('xyz/xyz_unittest.xyz','quip/gap/xyz') self.system_1 = self.multi_systems.systems['B1C9'] @@ -14,7 +14,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_temp0 = dpdata.MultiSystems.from_file(file_name='xyz/xyz_unittest.xyz', fmt='quip/gap/xyz') self.system_1 = self.system_temp0.systems['B5C7'] # .sort_atom_types() @@ -27,7 +27,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestQuipGapxyzsort1(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyzsort1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.sort.xyz','quip/gap/xyz') self.system_1 = self.multi_systems_1.systems['B5C7'] @@ -39,7 +39,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestQuipGapxyzsort2(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyzsort2(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.sort.xyz','quip/gap/xyz') self.system_1 = self.multi_systems_1.systems['B1C9'] @@ -51,7 +51,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestQuipGapxyzfield(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyzfield(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.field.xyz','quip/gap/xyz') self.system_1 = self.multi_systems_1.systems['B1C9'] @@ -63,7 +63,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestQuipGapxyzfield2(unittest.TestCase, CompLabeledSys): +class TestQuipGapxyzfield2(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.field.xyz','quip/gap/xyz') self.system_1 = self.multi_systems_1.systems['B5C7'] diff --git a/tests/test_replicate.py b/tests/test_replicate.py new file mode 100644 index 000000000..16ef8636b --- /dev/null +++ b/tests/test_replicate.py @@ -0,0 +1,22 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompSys, IsPBC + +class TestReplicate123(unittest.TestCase, CompSys, IsPBC): + def setUp (self) : + system_1_origin = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.system_1 = system_1_origin.replicate((1,2,3,)) + self.system_2 = dpdata.System('poscars/POSCAR.SiC.replicate123',fmt='vasp/poscar') + self.places = 6 + +class TestReplicate123_not_change_origin(unittest.TestCase, CompSys, IsPBC): + def setUp (self) : + self.system_1 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.system_1.replicate((1,2,3,)) + self.system_2 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') + self.places = 6 + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_system_append.py b/tests/test_system_append.py index 8dc5802aa..2a3d21cc5 100644 --- a/tests/test_system_append.py +++ b/tests/test_system_append.py @@ -4,8 +4,9 @@ from context import dpdata from comp_sys import CompSys from comp_sys import CompLabeledSys +from comp_sys import IsPBC, IsNoPBC -class TestVaspXmlAppend(unittest.TestCase, CompLabeledSys): +class TestVaspXmlAppend(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.places = 6 # rotated vasp computation, subject to numerical error @@ -23,7 +24,7 @@ def setUp (self) : self.system_2 = dpdata.LabeledSystem('poscars/vasprun.h2o.md.10.xml').sub_system(np.arange(0,10,2)) -class TestDifferentOrderAppend(unittest.TestCase, CompLabeledSys): +class TestDifferentOrderAppend(unittest.TestCase, CompLabeledSys, IsNoPBC): def setUp (self) : self.places = 6 self.e_places = 6 diff --git a/tests/test_to_ase.py b/tests/test_to_ase.py new file mode 100644 index 000000000..1cd7200a9 --- /dev/null +++ b/tests/test_to_ase.py @@ -0,0 +1,29 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompSys, IsPBC +try: + from ase import Atoms + from ase.io import write + exist_module=True +except: + exist_module=False + +@unittest.skipIf(not exist_module,"skip test_ase") +class TestASE(unittest.TestCase, CompSys, IsPBC): + + def setUp(self): + system_1 = dpdata.System() + system_1.from_lammps_lmp(os.path.join('poscars', 'conf.lmp'), type_map = ['O', 'H']) + write('tmp.POSCAR',system_1.to_ase_structure()[0],vasp5=True) + self.system_1=system_1 + self.system_2=dpdata.System('tmp.POSCAR') + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 6 + +if __name__ == '__main__': + unittest.main() + diff --git a/tests/test_to_list.py b/tests/test_to_list.py index b5251f847..e4c83cff3 100644 --- a/tests/test_to_list.py +++ b/tests/test_to_list.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys +from comp_sys import CompLabeledSys, IsPBC -class TestToList(unittest.TestCase, CompLabeledSys): +class TestToList(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : system = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', fmt = 'vasp/outcar') diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py new file mode 100644 index 000000000..5922828b4 --- /dev/null +++ b/tests/test_to_pymatgen.py @@ -0,0 +1,28 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompSys, IsPBC +try: + from pymatgen import Structure + exist_module=True +except: + exist_module=False + +@unittest.skipIf(not exist_module,"skip pymatgen") +class TestPymatgen(unittest.TestCase, CompSys, IsPBC): + + def setUp(self): + system_1 = dpdata.System() + system_1.from_lammps_lmp(os.path.join('poscars', 'conf.lmp'), type_map = ['O', 'H']) + system_1.to_pymatgen_structure()[0].to('poscar','tmp.POSCAR') + self.system_1=system_1 + self.system_2=dpdata.System('tmp.POSCAR') + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 6 + +if __name__ == '__main__': + unittest.main() + diff --git a/tests/test_vasp_outcar.py b/tests/test_vasp_outcar.py index 94c25e023..e2ab2e3db 100644 --- a/tests/test_vasp_outcar.py +++ b/tests/test_vasp_outcar.py @@ -2,9 +2,9 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompLabeledSys +from comp_sys import CompLabeledSys, IsPBC -class TestVaspOUTCAR(unittest.TestCase, CompLabeledSys): +class TestVaspOUTCAR(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.system_1 = dpdata.LabeledSystem() self.system_1.from_vasp_xml('poscars/vasprun.h2o.md.xml') @@ -15,7 +15,7 @@ def setUp (self) : self.f_places = 6 self.v_places = 4 -class TestVaspOUTCARTypeMap(unittest.TestCase, CompLabeledSys): +class TestVaspOUTCARTypeMap(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): sys0 = dpdata.LabeledSystem('poscars/OUTCAR.ch4.unconverged', fmt = 'vasp/outcar') sys0.data['atom_names'] = ['A', 'C', 'B', 'H', 'D'] @@ -29,7 +29,7 @@ def setUp(self): self.f_places = 6 self.v_places = 6 -class TestVaspOUTCARSkip(unittest.TestCase, CompLabeledSys): +class TestVaspOUTCARSkip(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : begin = 1 step = 3 diff --git a/tests/test_vasp_poscar_to_system.py b/tests/test_vasp_poscar_to_system.py index 0fa477693..f1248175e 100644 --- a/tests/test_vasp_poscar_to_system.py +++ b/tests/test_vasp_poscar_to_system.py @@ -2,7 +2,7 @@ import numpy as np import unittest from context import dpdata -from comp_sys import CompSys +from comp_sys import CompSys, IsPBC from poscars.poscar_ref_oh import TestPOSCARoh class TestPOSCARCart(unittest.TestCase, TestPOSCARoh): @@ -17,7 +17,7 @@ def setUp(self): self.system = dpdata.System() self.system.from_vasp_poscar(os.path.join('poscars', 'POSCAR.oh.d')) -class TestVaspPOSCARTypeMap(unittest.TestCase, CompSys): +class TestVaspPOSCARTypeMap(unittest.TestCase, CompSys, IsPBC): def setUp(self): sys0 = dpdata.System('poscars/POSCAR.oh.d', fmt = 'vasp/poscar') sys0.data['atom_names'] = ['A', 'H', 'B', 'O', 'D'] diff --git a/tests/test_vasp_xml.py b/tests/test_vasp_xml.py index 4db35027e..ed7ac6e80 100644 --- a/tests/test_vasp_xml.py +++ b/tests/test_vasp_xml.py @@ -4,8 +4,9 @@ from context import dpdata from comp_sys import CompSys from comp_sys import CompLabeledSys +from comp_sys import IsPBC -class TestVaspXml(unittest.TestCase, CompSys): +class TestVaspXml(unittest.TestCase, CompSys, IsPBC): def setUp (self) : self.places = 6 xml_sys = dpdata.LabeledSystem() @@ -18,7 +19,7 @@ def setUp (self) : self.system_2 = xml_sys.sub_system([-1]) -class TestVaspXmlRotSys(unittest.TestCase, CompLabeledSys): +class TestVaspXmlRotSys(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.places = 4 # rotated vasp computation, subject to numerical error @@ -29,7 +30,7 @@ def setUp (self) : self.system_2 = dpdata.LabeledSystem('poscars/vasprun.h2o.md.tribox.lower.xml') -class TestVaspXmlSkip(unittest.TestCase, CompLabeledSys): +class TestVaspXmlSkip(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : self.places = 6 # rotated vasp computation, subject to numerical error diff --git a/tests/test_water_ions.py b/tests/test_water_ions.py index 7027331c4..3a9436b6d 100644 --- a/tests/test_water_ions.py +++ b/tests/test_water_ions.py @@ -2,6 +2,12 @@ import numpy as np import unittest from context import dpdata +try: + import ase + import ase.neighborlist + exist_ase=True +except: + exist_ase=False class TestIons(unittest.TestCase): @@ -13,7 +19,6 @@ def setUp(self): self.system.data['coords'][0], self.system.data['atom_types']) - def test_ions_count(self) : no, noh, noh2, noh3, nh \ = dpdata.md.water.find_ions(self.system.data['atom_types'], self.bonds) @@ -25,6 +30,26 @@ def test_ions_count(self) : self.assertEqual(noh[0], 0) self.assertEqual(noh3[0], 51) + +@unittest.skipIf(not exist_ase, "skip TestAseComputeBond") +class TestAseComputeBond(unittest.TestCase): + def setUp(self): + self.system = dpdata.System() + self.system.from_lammps_lmp(os.path.join('poscars', 'conf.waterion.lmp'), + type_map = ['O', 'H']) + self.bonds = dpdata.md.water.compute_bonds_naive(self.system.data['cells'][0], + self.system.data['coords'][0], + self.system.data['atom_types']) + self.bonds_ase = dpdata.md.water.compute_bonds_ase(self.system.data['cells'][0], + self.system.data['coords'][0], + self.system.data['atom_types']) + + def test_bond_identity(self): + self.assertTrue(len(self.bonds), len(self.bonds_ase)) + for ii in range(len(self.bonds)): + self.assertTrue(set(self.bonds[ii]) == set(self.bonds_ase[ii])) + + if __name__ == '__main__': unittest.main()