auto_test update

auto_test/cmpt_02_elastic.py

@@ -68,7 +68,6 @@ def cmpt_deepmd_lammps(jdata, conf_dir, task_name) :
     lst_strain = []
     lst_stress = []
     for ii in lst_dfm_path :
-#        print(ii)
         strain = np.loadtxt(os.path.join(ii, 'strain.out'))
         stress = lammps.get_stress(os.path.join(ii, 'log.lammps'))
         # convert from pressure to stress
@@ -83,7 +82,7 @@ def cmpt_deepmd_lammps(jdata, conf_dir, task_name) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="cmpt 02.elastic")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/cmpt_03_vacancy.py

@@ -90,7 +90,7 @@ def cmpt_deepmd_lammps(jdata, conf_dir, supercell, task_name) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="cmpt 03.vacancy")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/cmpt_04_interstitial.py

@@ -122,7 +122,7 @@ def _cmpt_deepmd_lammps(jdata, conf_dir, supercell, insert_ele, task_name) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="cmpt 04.interstitial")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/cmpt_05_surf.py

@@ -74,7 +74,7 @@ def cmpt_deepmd_lammps(jdata, conf_dir, task_name, static = False) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="cmpt 05.surf")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/cmpt_06_phonon.py

@@ -0,0 +1,99 @@
+#!/usr/bin/env python3
+
+import os, re, argparse, filecmp, json, glob
+import subprocess as sp
+import numpy as np
+import lib.vasp as vasp
+import lib.lammps as lammps
+from phonopy import Phonopy
+from phonopy.structure.atoms import PhonopyAtoms
+import yaml
+import phonopy
+#from phonolammps import Phonolammps
+
+
+
+global_equi_name = '00.equi'
+global_task_name = '06.phonon'
+
+'''
+link poscar
+link potcar
+make incar
+'''
+def cmpt_vasp(jdata, conf_dir,opt) :
+    fp_params = jdata['vasp_params']
+    ecut = fp_params['ecut']
+    ediff = fp_params['ediff']
+    npar = fp_params['npar']
+    kpar = fp_params['kpar']
+    kspacing = fp_params['kspacing']
+    kgamma = fp_params['kgamma']
+    supercell_matrix=jdata['supercell_matrix']
+
+    conf_path = os.path.abspath(conf_dir)
+    task_path = re.sub('confs', global_task_name, conf_path)
+    task_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
+    cwd = os.getcwd()
+    os.chdir(task_path)
+    if os.path.isfile('vasprun.xml'):
+        os.system('phonopy --fc vasprun.xml')
+        os.system('phonopy --dim="%d %d %d" -c POSCAR-unitcell band.conf'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
+    else:
+        print('vasprun.xml No such file')
+    if opt=='Y':
+        ph = phonopy.load(supercell_matrix=supercell_matrix,primitive_matrix='auto',unitcell_filename="POSCAR-unitcell",force_constants_filename='FORCE_CONSTANTS')
+        ph.auto_band_structure(plot=True).show()
+
+
+def cmpt_deepmd_lammps(jdata, conf_dir,opt) :
+    deepmd_model_dir = jdata['deepmd_model_dir']
+    deepmd_type_map = jdata['deepmd_type_map']
+    ntypes = len(deepmd_type_map)    
+    deepmd_model_dir = os.path.abspath(deepmd_model_dir)
+    deepmd_models = glob.glob(os.path.join(deepmd_model_dir, '*pb'))
+    supercell_matrix=jdata['supercell_matrix']
+
+    conf_path = os.path.abspath(conf_dir)
+    task_path = re.sub('confs', global_task_name, conf_path)
+    task_path = os.path.join(task_path, 'deepmd')
+
+    os.chdir(task_path)
+    if os.path.isfile('FORCE_CONSTANTS'):
+        os.system('phonopy --dim="%d %d %d" -c POSCAR-unitcell band.conf'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
+    else:
+        print('FORCE_CONSTANTS No such file')
+    if opt=='Y':
+        ph = phonopy.load(supercell_matrix=supercell_matrix,primitive_matrix='auto',unitcell_filename="POSCAR-unitcell",force_constants_filename='FORCE_CONSTANTS')
+        ph.auto_band_structure(plot=True).show()
+
+
+def _main() :
+    parser = argparse.ArgumentParser(
+        description="cmpt 06.phonon")
+    parser.add_argument('TASK', type=str,
+                        help='the task of generation, vasp or lammps')
+    parser.add_argument('PARAM', type=str,
+                        help='json parameter file')
+    parser.add_argument('CONF', type=str,
+                        help='the path to conf')
+    parser.add_argument('OPT', type=str,
+                        help='show the band structue or not [Y/N]')
+    args = parser.parse_args()
+
+    with open (args.PARAM, 'r') as fp :
+        jdata = json.load (fp)
+
+#    print('generate %s task with conf %s' % (args.TASK, args.CONF))
+    if args.TASK == 'vasp':
+        cmpt_vasp(jdata, args.CONF,args.OPT)               
+    elif args.TASK == 'deepmd' :
+        cmpt_deepmd_lammps(jdata, args.CONF,args.OPT)
+    elif args.TASK == 'meam' :
+        cmpt_meam_lammps(jdata, args.CONF)
+    else :
+        raise RuntimeError("unknow task ", args.TASK)
+
+if __name__ == '__main__' :
+    _main()
+

auto_test/gen_01_eos.py

@@ -141,7 +141,7 @@ def make_deepmd_lammps (jdata, conf_dir) :
         print('# generate %s' % (vol_path))
         os.makedirs(vol_path, exist_ok = True)
         os.chdir(vol_path)
-        print(vol_path)
+        #print(vol_path)
         for ii in ['conf.lmp', 'conf.lmp'] + deepmd_models_name :
             if os.path.exists(ii) :
                 os.remove(ii)                
@@ -159,7 +159,7 @@ def make_deepmd_lammps (jdata, conf_dir) :
             os.symlink(os.path.relpath(ii), jj)
         # make lammps input
         scale = (vol / vpa) ** (1./3.)
-        fc = lammps.make_lammps_press_relax('conf.lmp', ntypes, scale, deepmd_models_name)
+        fc = lammps.make_lammps_press_relax('conf.lmp', ntypes, scale,lammps.inter_deepmd, deepmd_models_name)
         with open(os.path.join(vol_path, 'lammps.in'), 'w') as fp :
             fp.write(fc)
         os.chdir(cwd)
@@ -314,12 +314,12 @@ def _main() :
     if args.TASK == 'vasp':
         make_vasp(jdata, args.CONF)               
     elif args.TASK == 'deepmd' :
-        if args.fix_shape is not None :
+        if args.fix_shape :
             make_deepmd_lammps_fixv(jdata, args.CONF)
         else :
             make_deepmd_lammps(jdata, args.CONF)        
     elif args.TASK == 'meam' :
-        if args.fix_shape is not None :
+        if args.fix_shape:
             make_meam_lammps_fixv(jdata, args.CONF)
         else :
             raise RuntimeError("not implemented ", args.TASK)            

auto_test/gen_02_elastic.py

@@ -250,7 +250,7 @@ def make_meam_lammps(jdata, conf_dir) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="gen 02.elastic")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/gen_03_vacancy.py

@@ -234,7 +234,7 @@ def make_meam_lammps(jdata, conf_dir, supercell) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="gen 03.vacancy")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/gen_04_interstitial.py

@@ -405,7 +405,7 @@ def _make_meam_lammps(jdata, conf_dir, supercell, insert_ele, task_name) :
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="gen 04.interstitial")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,

auto_test/gen_05_surf.py

@@ -253,7 +253,7 @@ def make_meam_lammps(jdata, conf_dir, max_miller = 2, static = False, relax_box
 
 def _main() :
     parser = argparse.ArgumentParser(
-        description="gen 01.eos")
+        description="gen 05.surf")
     parser.add_argument('TASK', type=str,
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,