Support several CALYPSO run in different pressure in one iteration

.gitignore

@@ -42,3 +42,4 @@ dbconfig.json
 _build
 tests/generator/calypso_test_path
 doc/api/
+

README.md

@@ -590,15 +590,15 @@ The bold notation of key (such as **calypso_path**) means that it's a necessary
 | **model_devi_jobs["NameOfAtoms"]** | List of string |["Al","Cu"] | Parameter of CALYPSO input file, means the element species of structures to be generated. |
 | **model_devi_jobs["NumberOfAtoms"]** | List of int |[1,10] | Parameter of CALYPSO input file, means the number of atoms for each chemical species in one formula unit. |
 | **model_devi_jobs["NumberOfFormula"]** | List of int |[1,2] | Parameter of CALYPSO input file, means the range of formula unit per cell. |
-| **model_devi_jobs["Volume"]** | List of int |[300] | Parameter of CALYPSO input file, means the colume per formula unit(angstrom^3). |
+| **model_devi_jobs["Volume"]** | int | 300 | Parameter of CALYPSO input file, means the colume per formula unit(angstrom^3). |
 | **model_devi_jobs["DistanceOfIon"]** | List of float |[[ 1.48,1.44],[ 1.44,1.41]] | Parameter of CALYPSO input file, means minimal distance between atoms of each chemical species. Unit is in angstrom. |
-| **model_devi_jobs["PsoRatio"]** | List of float |[0.6] | Parameter of CALYPSO input file, means the proportion of the structures generated by PSO. |
-| **model_devi_jobs["PopSize"]** | List of int |[5] | Parameter of CALYPSO input file, means the number of structures to be generated in one step in CALYPSO. |
-| **model_devi_jobs["MaxStep"]** | List of int |[3] | Parameter of CALYPSO input file, means the number of max step in CALYPSO.|
-| **model_devi_jobs["ICode"]** | List of int |[13] | Parameter of CALYPSO input file, means the chosen of local optimization, 1 is vasp and 13 is ASE with dp.  |
+| **model_devi_jobs["PsoRatio"]** | float or int | 0.6 | Parameter of CALYPSO input file, means the proportion of the structures generated by PSO. |
+| **model_devi_jobs["PopSize"]** | int | 5 | Parameter of CALYPSO input file, means the number of structures to be generated in one step in CALYPSO. |
+| **model_devi_jobs["MaxStep"]** | int | 3 | Parameter of CALYPSO input file, means the number of max step in CALYPSO.|
+| **model_devi_jobs["ICode"]** | int | 13 | Parameter of CALYPSO input file, means the chosen of local optimization, 1 is vasp and 13 is ASE with dp.  |
 | **model_devi_jobs["Split"]** | String |"T" | Parameter of CALYPSO input file, means that generating structures and optimizing structures are split into two parts, in dpgen workflow, Split must be T. |
-| **model_devi_jobs["PSTRESS"]** | List of float |[0.001] | Same as PSTRESS in INCAR. |
-| **model_devi_jobs["fmax"]** | List of float |[0.01] | The convergence criterion is that the force on all individual atoms should be less than *fmax*. |
+| **model_devi_jobs["PSTRESS"]** | List of float or int |[0.001] | Same as PSTRESS in INCAR. |
+| **model_devi_jobs["fmax"]** | float | 0.01 | The convergence criterion is that the force on all individual atoms should be less than *fmax*. |
 | *in machine file*
 | **model_devi["deepmdkit_python"]** | String | "/home/zhenyu/soft/deepmd-kit/bin/python" | A python path with deepmd package. |
 | **model_devi["calypso_path"]** | string | "/home/zhenyu/workplace/debug" | The absolute path of calypso.x.|

dpgen/generator/lib/calypso_check_outcar.py

@@ -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()

dpgen/generator/lib/calypso_run_model_devi.py

@@ -70,9 +70,12 @@ def Modd(all_models,type_map):
                 pdata.to_vasp_poscar(os.path.join(put_poscar,'%s.poscar'%str(index)))
                 nopbc = pdata.nopbc
                 coord = pdata.data['coords']
-                cell  = pdata.data['cells']
+                cell  = pdata.data['cells'] if not nopbc else None
                 atom_types = pdata.data['atom_types']
-                devi = calc_model_devi(coord,cell,atom_types,graphs,nopbc=nopbc)
+                try:
+                    devi = calc_model_devi(coord,cell,atom_types,graphs,nopbc=nopbc)
+                except TypeError:
+                    devi = calc_model_devi(coord,cell,atom_types,graphs)
                 # ------------------------------------------------------------------------------------
                 # append min-distance in devi list
                 dis = pdata.to_ase_structure()[0].get_all_distances(mic=True)