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Merge pull request #216 from amcadmus/master
Merge recent development on devel into master
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| name: Mirror to Gitee Repo | ||
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| on: [ push, delete, create ] | ||
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| # Ensures that only one mirror task will run at a time. | ||
| concurrency: | ||
| group: git-mirror | ||
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| jobs: | ||
| git-mirror: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: wearerequired/git-mirror-action@v1 | ||
| env: | ||
| ORGANIZATION: deepmodeling | ||
| SSH_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }} | ||
| with: | ||
| source-repo: "https://github.com/deepmodeling/dpdata.git" | ||
| destination-repo: "git@gitee.com:deepmodeling/dpdata.git" |
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| .[docs] |
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| import os,sys | ||
| import numpy as np | ||
| from .scf import ry2ev, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords | ||
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| # Read in geometries from an ABACUS MD trajectory. | ||
| # The atomic coordinates are read in from generated files in OUT.XXXX. | ||
| # Energies, forces | ||
| # IMPORTANT: the program defaultly takes STRU input file as standard cell information, | ||
| # therefore the direct and cartesan coordinates read could be different from the ones in | ||
| # the output cif files!!! | ||
| # It is highly recommanded to use ORTHOGANAL coordinates in STRU file if you wish to get | ||
| # same coordinates in both dpdata and output cif files. | ||
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| def get_path_out(fname, inlines): | ||
| # This function is different from the same-name function in scf.py. | ||
| # This function returns OUT.XXXX's base directory. | ||
| path_out = os.path.join(fname, "OUT.ABACUS/") | ||
| for line in inlines: | ||
| if len(line)>0 and "suffix" in line and "suffix"==line.split()[0]: | ||
| suffix = line.split()[1] | ||
| path_out = os.path.join(fname, "OUT.%s/" % suffix) | ||
| break | ||
| return path_out | ||
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| def get_coord_dump_freq(inlines): | ||
| for line in inlines: | ||
| if len(line)>0 and "md_dumpmdfred" in line and "md_dumpmdfred" == line.split()[0]: | ||
| return int(line.split()[1]) | ||
| return 1 | ||
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| # set up a cell according to cell info in cif file. | ||
| # maybe useful later | ||
| ''' | ||
| def setup_cell(a, b, c, alpha, beta, gamma): | ||
| cell = np.zeros(3, 3) | ||
| cell[0, 0] = a | ||
| cell[1, 0] = b*np.cos(gamma/180*np.pi) | ||
| cell[1, 1] = b*np.sin(gamma/180*np.pi) | ||
| cell[2, 0] = c*np.cos(beta/180*np.pi) | ||
| cell[2, 1] = c*(b*np.cos(alpha/180*np.pi) - cell[1, 0]*np.cos(beta/180*np.pi))/cell[1, 1] | ||
| cell[2, 2] = np.sqrt(c**2 - cell[2, 0]**2 - cell[2, 1]**2) | ||
| return cell | ||
| ''' | ||
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| def get_single_coord_from_cif(pos_file, atom_names, natoms, cell): | ||
| assert(len(atom_names) == len(natoms)) | ||
| nele = len(atom_names) | ||
| total_natoms = sum(natoms) | ||
| coord = np.zeros([total_natoms, 3]) | ||
| a = 0 | ||
| b = 0 | ||
| c = 0 | ||
| alpha = 0 | ||
| beta = 0 | ||
| gamma = 0 | ||
| with open(pos_file, "r") as fp: | ||
| lines = fp.read().split("\n") | ||
| for line in lines: | ||
| if "_cell_length_a" in line: | ||
| a = float(line.split()[1]) | ||
| if "_cell_length_b" in line: | ||
| b = float(line.split()[1]) | ||
| if "_cell_length_c" in line: | ||
| c = float(line.split()[1]) | ||
| if "_cell_angle_alpha" in line: | ||
| alpha = float(line.split()[1]) | ||
| if "_cell_angle_beta" in line: | ||
| beta = float(line.split()[1]) | ||
| if "_cell_angle_gamma" in line: | ||
| gamma = float(line.split()[1]) | ||
| assert(a > 0 and b > 0 and c > 0 and alpha > 0 and beta > 0 and gamma > 0) | ||
| #cell = setup_cell(a, b, c, alpha, beta, gamma) | ||
| coord_lines = get_block(lines=lines, keyword="_atom_site_fract_z", skip=0, nlines = total_natoms) | ||
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| ia_idx = 0 | ||
| for it in range(nele): | ||
| for ia in range(natoms[it]): | ||
| coord_line = coord_lines[ia_idx].split() | ||
| assert(coord_line[0] == atom_names[it]) | ||
| coord[ia_idx, 0] = float(coord_line[1]) | ||
| coord[ia_idx, 1] = float(coord_line[2]) | ||
| coord[ia_idx, 2] = float(coord_line[3]) | ||
| ia_idx+=1 | ||
| coord = np.matmul(coord, cell) | ||
| # important! Coordinates are converted to Cartesian coordinate. | ||
| return coord | ||
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| def get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell): | ||
| total_natoms = sum(natoms) | ||
| #cell = np.zeros(ndump, 3, 3) | ||
| coords = np.zeros([ndump, total_natoms, 3]) | ||
| pos_file = os.path.join(path_out, "STRU_READIN_ADJUST.cif") | ||
| # frame 0 file is different from any other frames | ||
| coords[0] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) | ||
| for dump_idx in range(1, ndump): | ||
| pos_file = os.path.join(path_out, "md_pos_%d.cif" %(dump_idx*dump_freq)) | ||
| #print("dump_idx = %s" %dump_idx) | ||
| coords[dump_idx] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) | ||
| return coords | ||
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| def get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names): | ||
| stress = None | ||
| total_natoms = sum(natoms) | ||
| for line in inlines: | ||
| if len(line)>0 and "stress" in line and "stress" == line.split()[0] and "1" == line.split()[1]: | ||
| stress = np.zeros([ndump, 3, 3]) | ||
| break | ||
| if type(stress) != np.ndarray: | ||
| print("The ABACUS program has no stress output. Stress will not be read.") | ||
| nenergy = 0 | ||
| nforce = 0 | ||
| nstress = 0 | ||
| energy = np.zeros(ndump) | ||
| force = np.zeros([ndump, total_natoms, 3]) | ||
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| for line_idx, line in enumerate(outlines): | ||
| if "final etot is" in line: | ||
| if nenergy%dump_freq == 0: | ||
| energy[int(nenergy/dump_freq)] = float(line.split()[-2]) | ||
| nenergy+=1 | ||
| if "TOTAL-FORCE (eV/Angstrom)" in line: | ||
| for iatom in range(0, total_natoms): | ||
| force_line = outlines[line_idx+5+iatom] | ||
| atom_force = [float(i) for i in force_line.split()[1:]] | ||
| assert(len(atom_force) == 3) | ||
| atom_force = np.array(atom_force) | ||
| if nforce%dump_freq == 0: | ||
| force[int(nforce/dump_freq), iatom] = atom_force | ||
| nforce+=1 | ||
| assert(nforce==nenergy) | ||
| if "TOTAL-STRESS (KBAR)" in line: | ||
| for idx in range(0, 3): | ||
| stress_line = outlines[line_idx+4+idx] | ||
| single_stress = [float(i) for i in stress_line.split()] | ||
| if len(single_stress) != 3: | ||
| print(single_stress) | ||
| assert(len(single_stress) == 3) | ||
| single_stress = np.array(single_stress) | ||
| if nstress%dump_freq == 0: | ||
| stress[int(nstress/dump_freq), idx] = single_stress | ||
| nstress+=1 | ||
| assert(nstress==nforce) | ||
| if type(stress) == np.ndarray: | ||
| stress *= kbar2evperang3 | ||
| return energy, force, stress | ||
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| def get_frame (fname): | ||
| if type(fname) == str: | ||
| # if the input parameter is only one string, it is assumed that it is the | ||
| # base directory containing INPUT file; | ||
| path_in = os.path.join(fname, "INPUT") | ||
| else: | ||
| raise RuntimeError('invalid input') | ||
| with open(path_in, 'r') as fp: | ||
| inlines = fp.read().split('\n') | ||
| geometry_path_in = get_geometry_in(fname, inlines) # base dir of STRU | ||
| path_out = get_path_out(fname, inlines) | ||
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| with open(geometry_path_in, 'r') as fp: | ||
| geometry_inlines = fp.read().split('\n') | ||
| celldm, cell = get_cell(geometry_inlines) | ||
| atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) | ||
| # This coords is not to be used. | ||
| dump_freq = get_coord_dump_freq(inlines = inlines) | ||
| ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) | ||
| # number of dumped geometry files | ||
| coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) | ||
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| # TODO: Read in energies, forces and pressures. | ||
| with open(os.path.join(path_out, "running_md.log"), 'r') as fp: | ||
| outlines = fp.read().split('\n') | ||
| energy, force, stress = get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names) | ||
| if type(stress) == np.ndarray: | ||
| stress *= np.linalg.det(cell) | ||
| data = {} | ||
| data['atom_names'] = atom_names | ||
| data['atom_numbs'] = natoms | ||
| data['atom_types'] = types | ||
| data['cells'] = np.zeros([ndump, 3, 3]) | ||
| for idx in range(ndump): | ||
| data['cells'][:, :, :] = cell | ||
| data['coords'] = coords | ||
| data['energies'] = energy | ||
| data['forces'] = force | ||
| data['virials'] = stress | ||
| if type(data['virials']) != np.ndarray: | ||
| del data['virials'] | ||
| data['orig'] = np.zeros(3) | ||
|
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| return data |
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