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Support several CALYPSO run in different pressure in one iteration (#814
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@@ -42,3 +42,4 @@ dbconfig.json | |
| _build | ||
| tests/generator/calypso_test_path | ||
| doc/api/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,107 +1,104 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
|
|
||
| import numpy as np | ||
| import os,sys,glob,time | ||
| from deepmd.calculator import DP | ||
| from ase.io import read | ||
| import numpy as np | ||
| import os,sys,glob,time | ||
| from deepmd.calculator import DP | ||
| from ase.io import read | ||
|
|
||
| ''' | ||
| check if structure optimization worked well | ||
| if not, this script will generate a fake outcar | ||
| ''' | ||
| def Get_Element_Num(elements): | ||
|
|
||
| def Get_Element_Num(elements): | ||
| '''Using the Atoms.symples to Know Element&Num''' | ||
| element = [] | ||
| ele = {} | ||
| element.append(elements[0]) | ||
| for x in elements: | ||
| if x not in element : | ||
| element.append(x) | ||
| for x in element: | ||
| ele[x] = elements.count(x) | ||
| return element, ele | ||
|
|
||
| def Write_Contcar(element, ele, lat, pos): | ||
| '''Write CONTCAR''' | ||
| f = open('CONTCAR','w') | ||
| f.write('ASE-DPKit-FAILED-nan\n') | ||
| f.write('1.0\n') | ||
| for i in range(3): | ||
| f.write('%15.10f %15.10f %15.10f\n' % tuple(lat[i])) | ||
| for x in element: | ||
| f.write(x + ' ') | ||
| f.write('\n') | ||
| for x in element: | ||
| f.write(str(ele[x]) + ' ') | ||
| f.write('\n') | ||
| f.write('Direct\n') | ||
| na = sum(ele.values()) | ||
| dpos = np.dot(pos,np.linalg.inv(lat)) | ||
| for i in range(na): | ||
| f.write('%15.10f %15.10f %15.10f\n' % tuple(dpos[i])) | ||
|
|
||
| def Write_Outcar(element, ele, volume, lat, pos, ene, force, stress,pstress): | ||
| '''Write OUTCAR''' | ||
| f = open('OUTCAR','w') | ||
| for x in element: | ||
| f.write('VRHFIN =' + str(x) + '\n') | ||
| f.write('ions per type =') | ||
| for x in element: | ||
| f.write('%5d' % ele[x]) | ||
| #f.write('\nvolume of cell :\n') | ||
| element = [] | ||
| ele = {} | ||
| element.append(elements[0]) | ||
| for x in elements: | ||
| if x not in element : | ||
| element.append(x) | ||
| for x in element: | ||
| ele[x] = elements.count(x) | ||
| return element, ele | ||
|
|
||
| def Write_Contcar(element, ele, lat, pos): | ||
| '''Write CONTCAR''' | ||
| f = open('CONTCAR','w') | ||
| f.write('ASE-DPKit-FAILED-nan\n') | ||
| f.write('1.0\n') | ||
| for i in range(3): | ||
| f.write('%15.10f %15.10f %15.10f\n' % tuple(lat[i])) | ||
| for x in element: | ||
| f.write(x + ' ') | ||
| f.write('\n') | ||
| for x in element: | ||
| f.write(str(ele[x]) + ' ') | ||
| f.write('\n') | ||
| f.write('Direct\n') | ||
| na = sum(ele.values()) | ||
| dpos = np.dot(pos,np.linalg.inv(lat)) | ||
| for i in range(na): | ||
| f.write('%15.10f %15.10f %15.10f\n' % tuple(dpos[i])) | ||
|
|
||
| def Write_Outcar(element, ele, volume, lat, pos, ene, force, stress,pstress): | ||
| '''Write OUTCAR''' | ||
| f = open('OUTCAR','w') | ||
| for x in element: | ||
| f.write('VRHFIN =' + str(x) + '\n') | ||
| f.write('ions per type =') | ||
| for x in element: | ||
| f.write('%5d' % ele[x]) | ||
| f.write('\nDirection XX YY ZZ XY YZ ZX\n') | ||
| f.write('in kB') | ||
| f.write('%15.6f' % stress[0]) | ||
| f.write('%15.6f' % stress[1]) | ||
| f.write('%15.6f' % stress[2]) | ||
| f.write('%15.6f' % stress[3]) | ||
| f.write('%15.6f' % stress[4]) | ||
| f.write('%15.6f' % stress[5]) | ||
| f.write('\n') | ||
| ext_pressure = np.sum(stress[0] + stress[1] + stress[2])/3.0 - pstress | ||
| f.write('in kB') | ||
| f.write('%15.6f' % stress[0]) | ||
| f.write('%15.6f' % stress[1]) | ||
| f.write('%15.6f' % stress[2]) | ||
| f.write('%15.6f' % stress[3]) | ||
| f.write('%15.6f' % stress[4]) | ||
| f.write('%15.6f' % stress[5]) | ||
| f.write('\n') | ||
| ext_pressure = np.sum(stress[0] + stress[1] + stress[2])/3.0 - pstress | ||
| f.write('external pressure = %20.6f kB Pullay stress = %20.6f kB\n'% (ext_pressure, pstress)) | ||
| f.write('volume of cell : %20.6f\n' % volume) | ||
| f.write('direct lattice vectors\n') | ||
| for i in range(3): | ||
| f.write('%10.6f %10.6f %10.6f\n' % tuple(lat[i])) | ||
| f.write('POSITION TOTAL-FORCE(eV/Angst)\n') | ||
| f.write('-------------------------------------------------------------------\n') | ||
| na = sum(ele.values()) | ||
| for i in range(na): | ||
| f.write('%15.6f %15.6f %15.6f' % tuple(pos[i])) | ||
| f.write('%15.6f %15.6f %15.6f\n' % tuple(force[i])) | ||
| f.write('-------------------------------------------------------------------\n') | ||
| f.write('energy without entropy= %20.6f %20.6f\n' % (ene, ene)) | ||
| enthalpy = ene + pstress * volume / 1602.17733 | ||
| f.write('enthalpy is TOTEN = %20.6f %20.6f\n' % (enthalpy, enthalpy)) | ||
|
|
||
| def check(): | ||
|
|
||
| from deepmd.calculator import DP | ||
| from ase.io import read | ||
| model_path = sys.argv[1] | ||
| Model_List = glob.glob('%s/graph*pb'%model_path) | ||
| calc = DP(model='%s'%(Model_List[0])) # init the model before iteration | ||
|
|
||
| to_be_opti = read('POSCAR') | ||
| to_be_opti.calc = calc | ||
| # --------------------------------- | ||
| # for failed outcar | ||
| atoms_symbols_f = to_be_opti.get_chemical_symbols() | ||
| element_f, ele_f = Get_Element_Num(atoms_symbols_f) | ||
| atoms_vol_f = to_be_opti.get_volume() | ||
| atoms_stress_f = to_be_opti.get_stress() | ||
| atoms_stress_f = atoms_stress_f/(0.01*0.6242) | ||
| atoms_lat_f = to_be_opti.cell | ||
| atoms_pos_f = to_be_opti.positions | ||
| atoms_force_f = to_be_opti.get_forces() | ||
| atoms_ene_f = 610612509 | ||
| # --------------------------------- | ||
| Write_Contcar(element_f, ele_f, atoms_lat_f, atoms_pos_f) | ||
| f.write('volume of cell : %20.6f\n' % volume) | ||
| f.write('direct lattice vectors\n') | ||
| for i in range(3): | ||
| f.write('%10.6f %10.6f %10.6f\n' % tuple(lat[i])) | ||
| f.write('POSITION TOTAL-FORCE(eV/Angst)\n') | ||
| f.write('-------------------------------------------------------------------\n') | ||
| na = sum(ele.values()) | ||
| for i in range(na): | ||
| f.write('%15.6f %15.6f %15.6f' % tuple(pos[i])) | ||
| f.write('%15.6f %15.6f %15.6f\n' % tuple(force[i])) | ||
| f.write('-------------------------------------------------------------------\n') | ||
| f.write('energy without entropy= %20.6f %20.6f\n' % (ene, ene)) | ||
| enthalpy = ene + pstress * volume / 1602.17733 | ||
| f.write('enthalpy is TOTEN = %20.6f %20.6f\n' % (enthalpy, enthalpy)) | ||
|
|
||
| def check(): | ||
|
|
||
| from deepmd.calculator import DP | ||
| from ase.io import read | ||
| calc = DP(model='../graph.000.pb') # init the model before iteration | ||
|
|
||
| to_be_opti = read('POSCAR') | ||
| to_be_opti.calc = calc | ||
| # --------------------------------- | ||
| # for failed outcar | ||
| atoms_symbols_f = to_be_opti.get_chemical_symbols() | ||
| element_f, ele_f = Get_Element_Num(atoms_symbols_f) | ||
| atoms_vol_f = to_be_opti.get_volume() | ||
| atoms_stress_f = to_be_opti.get_stress() | ||
| atoms_stress_f = atoms_stress_f/(0.01*0.6242) | ||
| atoms_lat_f = to_be_opti.cell | ||
| atoms_pos_f = to_be_opti.positions | ||
| atoms_force_f = to_be_opti.get_forces() | ||
| atoms_ene_f = 610612509 | ||
| # --------------------------------- | ||
| Write_Contcar(element_f, ele_f, atoms_lat_f, atoms_pos_f) | ||
| Write_Outcar(element_f, ele_f, atoms_vol_f, atoms_lat_f, atoms_pos_f,atoms_ene_f, atoms_force_f, atoms_stress_f * -10.0, 0) | ||
|
|
||
| cwd = os.getcwd() | ||
| if not os.path.exists(os.path.join(cwd,'OUTCAR')): | ||
| check() | ||
| cwd = os.getcwd() | ||
| if not os.path.exists(os.path.join(cwd,'OUTCAR')): | ||
| check() |
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