Support several CALYPSO run in different pressure in one iteration

.gitignore

@@ -41,4 +41,4 @@ dbconfig.json
 .idea/*
 _build
 tests/generator/calypso_test_path
-doc/api/
+doc/api/

README.md

@@ -591,15 +591,15 @@ 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/make_calypso.py

@@ -3,6 +3,7 @@
 import shutil
 import json
 import numpy as np
+from dpgen.generator.lib.utils import create_path
 
 def make_calypso_input(nameofatoms,numberofatoms,
                            numberofformula,volume,
@@ -24,7 +25,7 @@ def make_calypso_input(nameofatoms,numberofatoms,
     assert numberofformula != None  or len(numberofformula) == 2 or type(numberofformula) == type([1,2])
     ret+= "NumberOfFormula = %s\n"%(' '.join(list(map(str,numberofformula))))
     ret+= "# The volume per formula unit. Unit is in angstrom^3.\n"
-    ret+= "Volume = %s\n"%(volume[0])
+    ret+= "Volume = %s\n"%(volume)
     ret+= "# Minimal distance between atoms of each chemical species. Unit is in angstrom.\n"
     assert len(distanceofion) == len(nameofatoms) #"check distance of ions and the number of atoms"
     assert len(distanceofion[0]) == len(nameofatoms)
@@ -37,14 +38,14 @@ def make_calypso_input(nameofatoms,numberofatoms,
     ret+= "# Ialgo = 1 for Global PSO\n"
     ret+= "# Ialgo = 2 for Local PSO (default value)\n"
     ret+= "# The proportion of the structures generated by PSO.\n"
-    assert (0 <=  psoratio[0] <= 1  )
-    ret+= "PsoRatio = %s\n"%(psoratio[0])
+    assert (0 <=  psoratio <= 1  )
+    ret+= "PsoRatio = %s\n"%(psoratio)
     ret+= "# The population size. Normally, it has a larger number for larger systems.\n"
-    assert popsize[0] != None  or popsize!=None or type(popsize) == type([0,1]) or type(popsize[0]) == type(0)
-    ret+= "PopSize = %d\n"%(popsize[0])
-    assert maxstep[0] != None  or maxstep!=None or type(maxstep) == type([0,1]) or type(maxstep[0]) == type(0)
+    assert popsize != None or type(popsize) == type(0)
+    ret+= "PopSize = %d\n"%(popsize)
+    assert maxstep != None or type(maxstep) == type(0)
     ret+= "# The Max step for iteration\n"
-    ret+= "MaxStep = %d\n"%(maxstep[0])
+    ret+= "MaxStep = %d\n"%(maxstep)
     ret+= "#It determines which method should be adopted in generation the random structure. \n"                             
     ret+= "GenType= 1 \n"
     ret+= "# 1 under symmetric constraints\n"
@@ -53,8 +54,8 @@ def make_calypso_input(nameofatoms,numberofatoms,
     ret+= "# 0 combination of all method\n"
     ret+= "# If GenType=3 or 4, it determined the small unit to grow the whole structure\n"
     ret+= "# It determines which local optimization method should be interfaced in the simulation.\n"
-    assert icode != None  or type(icode) == type([0,1]) or type(icode[0]) == type(0)
-    ret+= "ICode= %d\n"%(icode[0])
+    assert icode != None  or type(icode) == type(0)
+    ret+= "ICode= %d\n"%(icode)
     ret+= "# ICode= 1 interfaced with VASP\n"
     ret+= "# ICode= 2 interfaced with SIESTA\n"
     ret+= "# ICode= 3 interfaced with GULP\n"
@@ -75,18 +76,18 @@ def make_calypso_input(nameofatoms,numberofatoms,
     ret+= "NumberOfParallel = 4\n"
     assert split != None 
     ret+= "Split = %s\n"%(split)
-    assert pstress != None  or type(pstress) == type([200])
-    ret+= "PSTRESS = %f\n"%(pstress[0])
-    assert fmax != None  or type(fmax) == type([200])
-    ret+= "fmax = %f\n"%(fmax[0])
+    assert pstress != None  or type(pstress) == type(200) or type(pstress) == type(0.001)
+    ret+= "PSTRESS = %f\n"%(pstress)
+    assert fmax != None  or type(fmax) == type(0.01)
+    ret+= "fmax = %f\n"%(fmax)
     ret+= "################################ End of The Basic Parameters of CALYPSO #######################\n"
     if vsc == 'T':
         assert len(ctrlrange) == len(nameofatoms) #'check distance of ions and the number of atoms'
         ret+= "##### The Parameters For Variational Stoichiometry  ##############\n"
         ret+= "## If True, Variational Stoichiometry structure prediction is performed\n"
         ret+= "VSC = %s\n"%(vsc)
         ret+= "# The Max Number of Atoms in unit cell\n"
-        ret+= "MaxNumAtom = %s\n"%(maxnumatom[0])
+        ret+= "MaxNumAtom = %s\n"%(maxnumatom)
         ret+= "# The Variation Range for each type atom \n"
         ret+= "@CtrlRange\n"                                                                                                      
         for ttemp in ctrlrange:
@@ -95,18 +96,19 @@ def make_calypso_input(nameofatoms,numberofatoms,
         ret+= "###################End Parameters for VSC ##########################\n"
     return ret
 
-def _make_model_devi_buffet(jdata,calypso_run_opt_path):
+def _make_model_devi_buffet(jdata,caly_run_opt_path):
 
     calypso_input_path = jdata.get('calypso_input_path')
-    shutil.copyfile(os.path.join(calypso_input_path,'input.dat'),os.path.join(calypso_run_opt_path, 'input.dat'))
+    shutil.copyfile(os.path.join(calypso_input_path,'input.dat'),os.path.join(caly_run_opt_path[0], 'input.dat'))
 
-def _make_model_devi_native_calypso(iter_index,model_devi_jobs, calypso_run_opt_path):
+def _make_model_devi_native_calypso(iter_index,model_devi_jobs, caly_run_opt_path):
 
     for iiidx, jobbs in enumerate(model_devi_jobs):
         if iter_index in jobbs.get('times'):
             cur_job = model_devi_jobs[iiidx]
 
-    work_path = os.path.dirname(calypso_run_opt_path)
+    work_path = os.path.dirname(caly_run_opt_path[0])
+    # cur_job.json
     with open(os.path.join(work_path, 'cur_job.json'), 'w') as outfile:
         json.dump(cur_job, outfile, indent = 4)
 
@@ -116,34 +118,37 @@ def _make_model_devi_native_calypso(iter_index,model_devi_jobs, calypso_run_opt_
     numberofformula = cur_job.get('NumberOfFormula',[1,1])
     volume = cur_job.get('Volume')
     distanceofion = cur_job.get('DistanceOfIon')
-    psoratio = cur_job.get('PsoRatio')
-    popsize = cur_job.get('PopSize')
-    maxstep = cur_job.get('MaxStep')
-    icode = cur_job.get('ICode',[1])
+    psoratio = cur_job.get('PsoRatio', 0.6)
+    popsize = cur_job.get('PopSize', 30)
+    maxstep = cur_job.get('MaxStep', 5)
+    icode = cur_job.get('ICode',1)
     split = cur_job.get('Split','T')
+    # Cluster
+
+    # 2D
+
     # VSC Control
     maxnumatom = None
     ctrlrange = None
     vsc = cur_job.get('VSC','F')
     if vsc == 'T':
         maxnumatom = cur_job.get('MaxNumAtom')
         ctrlrange = cur_job.get('CtrlRange')
-
     # Optimization
+    fmax = cur_job.get('fmax',0.01)
+    # pstress is a List which contains the target stress
     pstress = cur_job.get('PSTRESS',[0.001])
-    fmax = cur_job.get('fmax',[0.01])
-
-    # Cluster
-
-    # 2D
-
-    file_c = make_calypso_input(nameofatoms,numberofatoms,
+    # pressures
+    for press_idx, temp_caly_run_opt_path in enumerate(caly_run_opt_path):
+        # cur_press
+        cur_press = pstress[press_idx]
+        file_c = make_calypso_input(nameofatoms,numberofatoms,
                                numberofformula,volume,
                                distanceofion,psoratio,popsize,
                                maxstep,icode,split,vsc,
-                               maxnumatom,ctrlrange,pstress,fmax)
-    with open(os.path.join(calypso_run_opt_path, 'input.dat'), 'w') as cin :
-        cin.write(file_c)
+                               maxnumatom,ctrlrange,cur_press,fmax)
+        with open(os.path.join(temp_caly_run_opt_path, 'input.dat'), 'w') as cin :
+            cin.write(file_c)
 
 def write_model_devi_out(devi, fname):
     assert devi.shape[1] == 8