Merge pull request #5 from deepmodeling/devel

sync

.travis.yml

@@ -3,6 +3,15 @@ python:
   - "3.6.3"
   - "3.6-dev"  # 3.6 development branch
 # command to install dependencies
+env:
+  matrix:
+  - PYMATGEN_VERSION=2017.9.1
+  - PYMATGEN_VERSION=2018.1.19
+  - PYMATGEN_VERSION=2019.1.13
+  - PYMATGEN_VERSION=2019.7.30
+before_install:
+  - pip install --upgrade pip
+  - pip install pymatgen==$PYMATGEN_VERSION
 install:
   - pip install .
 # command to run tests

dpgen/data/gen.py

@@ -12,6 +12,7 @@
 import time
 import dpdata
 import numpy as np
+from dpgen import dlog
 import os,json,shutil,re,glob,argparse,dpdata
 import numpy as np
 import subprocess as sp
@@ -21,6 +22,7 @@
 import dpgen.data.tools.diamond as diamond
 import dpgen.data.tools.sc as sc
 from pymatgen import Structure
+from dpgen.remote.decide_machine import decide_train_machine, decide_fp_machine, decide_model_devi_machine
 from dpgen.remote.RemoteJob import SSHSession, JobStatus, SlurmJob, PBSJob, CloudMachineJob
 from dpgen import ROOT_PATH
 
@@ -351,7 +353,7 @@ def make_vasp_relax (jdata, mdata) :
     os.chdir(work_dir)
     #replace('INCAR', 'ENCUT=.*', 'ENCUT=%f' % encut)
     #replace('INCAR', 'ISIF=.*', 'ISIF=3')
-    #replace('INCAR', 'KSPACING=.*', 'KSPACING=%f' % kspacing)
+    #replace('INCAR', 'KSPACING=.*from dpgen.remote.decide_machine import decide_train_machine, decide_fp_machine, decide_model_devi_machine', 'KSPACING=%f' % kspacing)
     #if kgamma :
     #    replace('INCAR', 'KGAMMA=.*', 'KGAMMA=T')
     #else :
@@ -537,11 +539,17 @@ def coll_vasp_md(jdata) :
             for kk in range(pert_numb) :
                 path_work = os.path.join("scale-%.3f" % jj, "%06d" % kk)
                 outcar = os.path.join(path_work, 'OUTCAR')
+                #print("OUTCAR",outcar)
                 if os.path.isfile(outcar) :
+                    #print("*"*40)
                     with open(outcar, 'r') as fin:
                         nforce = fin.read().count('TOTAL-FORCE')
+                    #print("nforce is", nforce)
+                    #print("md_nstep", md_nstep)
                     if nforce == md_nstep :
                         valid_outcars.append(outcar)
+                    else:
+                        print("WARNING : in directory %s nforce in OUTCAR is not equal to settings in INCAR"%(os.getcwd()))
         arg_cvt = " "
         if len(valid_outcars) == 0:
             raise RuntimeError("MD dir: %s: find no valid outcar in sys %s, "
@@ -629,8 +637,8 @@ def run_vasp_relax(jdata, mdata, ssh_sess):
             forward_common_files=['cvasp.py']
     relax_tasks = glob.glob(os.path.join(work_dir, "sys-*"))
     relax_tasks.sort()
-    print("work_dir",work_dir)
-    print("relax_tasks",relax_tasks)
+    #print("work_dir",work_dir)
+    #print("relax_tasks",relax_tasks)
     if len(relax_tasks) == 0:
         return
 
@@ -673,22 +681,22 @@ def run_vasp_md(jdata, mdata, ssh_sess):
     path_md = os.path.abspath(path_md)
     cwd = os.getcwd()
     assert(os.path.isdir(path_md)), "md path should exists"
-    os.chdir(path_md)
-    md_tasks = glob.glob('sys-*/scale*/00*')
+    md_tasks = glob.glob(os.path.join(work_dir, 'sys-*/scale*/00*'))
     md_tasks.sort()
 
-    os.chdir(cwd)
-
     if len(md_tasks) == 0:
         return
 
     md_run_tasks = []
     for ii in md_tasks : 
         if not _vasp_check_fin(ii):
             md_run_tasks.append(ii)
-    run_tasks = [ii for ii in md_run_tasks]
 
-    print("run_tasks",run_tasks)
+
+    run_tasks = [ii.replace(work_dir+"/", "") for ii in md_run_tasks]
+    #print("md_work_dir", work_dir)
+    #print("run_tasks",run_tasks)
+
     assert (machine_type == "slurm" or machine_type =="Slurm"), "Currently only support for Slurm!"
     _group_slurm_jobs(ssh_sess,
                            fp_resources,
@@ -699,7 +707,6 @@ def run_vasp_md(jdata, mdata, ssh_sess):
                            forward_common_files,
                            forward_files,
                            backward_files)
-
 
 
 
@@ -718,28 +725,55 @@ def gen_init_bulk(args) :
             jdata = json.load (fp)
         with open (args.MACHINE, "r") as fp:
             mdata = json.load(fp)
-
-    out_dir = out_dir_name(jdata)
-
-    fp_machine = mdata['fp_machine']    
+    # Selecting a proper machine
+    mdata = decide_fp_machine(mdata)
+    fp_machine = mdata['fp_machine']
     fp_ssh_sess = SSHSession(fp_machine)  
+    # Decide work path
+    out_dir = out_dir_name(jdata)
     jdata['out_dir'] = out_dir
+    print ("# working dir %s" % out_dir)
+    # Decide whether to use a given poscar
+    from_poscar = False 
+    if 'from_poscar' in jdata :
+        from_poscar = jdata['from_poscar']
+    # Verify md_nstep
+    md_nstep_jdata = jdata["md_nstep"]
+    try:
+        md_incar = jdata['md_incar']
+        if os.path.isfile(md_incar):
+            with open(md_incar , "r") as fr:
+                md_incar_lines = fr.readlines()
+            nsw_flag = False
+            for incar_line in md_incar_lines:
+                line = incar_line.split()
+                if "NSW" in line:
+                    nsw_flag = True
+                    nsw_steps = int(incar_line.split()[-1])
+                    break
+            #print("nsw_steps is", nsw_steps)
+            #print("md_nstep_jdata is", md_nstep_jdata)
+            if nsw_flag:
+                if (nsw_steps != md_nstep_jdata):
+                    print("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
+                    print("MD steps in PARAM is %d"%(md_nstep_jdata))
+                    print("MD steps in md_incar is %d"%(nsw_steps))
+                    print("DP-GEN will use settings in md_incar!")
+                    jdata['md_nstep'] = nsw_steps
+    except:
+        pass
     ## correct element name 
     temp_elements = []
     for ele in jdata['elements']:
         temp_elements.append(ele[0].upper() + ele[1:])
     jdata['elements'] = temp_elements
+    print("Elements are", jdata['elements'])
 
-    from_poscar = False 
-    if 'from_poscar' in jdata :
-        from_poscar = jdata['from_poscar']
-    print ("# working dir %s" % out_dir)
-
+    ## Iteration 
     stage_list = [int(i) for i in jdata['stages']]
-
-
     for stage in stage_list:
         if stage == 1 :
+            print("Current stage is 1, relax")
             create_path(out_dir)
             shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
             if from_poscar :
@@ -748,15 +782,18 @@ def gen_init_bulk(args) :
                 make_unit_cell(jdata)
                 make_super_cell(jdata)
                 place_element(jdata)
-            make_vasp_relax(jdata, mdata)      
+            make_vasp_relax(jdata, mdata)
             run_vasp_relax(jdata, mdata, fp_ssh_sess)
         elif stage == 2 :
+            print("Current stage is 2, perturb and scale")
             make_scale(jdata)
             pert_scaled(jdata)
         elif stage == 3 :
+            print("Current stage is 3, run a short md")
             make_vasp_md(jdata)
             run_vasp_md(jdata, mdata, fp_ssh_sess)
         elif stage == 4 :
+            print("Current stage is 4, collect data")
             coll_vasp_md(jdata)
         else :
             raise RuntimeError("unknown stage %d" % stage)
@@ -781,19 +818,55 @@ def _main() :
             jdata = json.load (fp)
         with open (args.MACHINE, "r") as fp:
             mdata = json.load(fp)
-
-
+    # Selecting a proper machine
+    mdata = decide_fp_machine(mdata)
+    fp_machine = mdata['fp_machine']
+    fp_ssh_sess = SSHSession(fp_machine)  
+    # Decide work path
     out_dir = out_dir_name(jdata)
     jdata['out_dir'] = out_dir
+    print ("# working dir %s" % out_dir)
+    # Decide whether to use a given poscar
     from_poscar = False 
     if 'from_poscar' in jdata :
         from_poscar = jdata['from_poscar']
-    print ("# working dir %s" % out_dir)
+    # Verify md_nstep
+    md_nstep_jdata = jdata["md_nstep"]
+    try:
+        md_incar = jdata['md_incar']
+        if os.path.isfile(md_incar):
+            with open(md_incar , "r") as fr:
+                md_incar_lines = fr.readlines()
+            nsw_flag = False
+            for incar_line in md_incar_lines:
+                line = incar_line.split()
+                if "NSW" in line:
+                    nsw_flag = True
+                    nsw_steps = int(incar_line.split()[-1])
+                    break
+            #print("nsw_steps is", nsw_steps)
+            #print("md_nstep_jdata is", md_nstep_jdata)
+            if nsw_flag:
+                if (nsw_steps != md_nstep_jdata):
+                    print("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
+                    print("MD steps in PARAM is %d"%(md_nstep_jdata))
+                    print("MD steps in md_incar is %d"(nsw_steps))
+                    print("DP-GEN will use settings in md_incar!")
+                    jdata['md_nstep'] = nsw_steps
+    except:
+        pass
+    ## correct element name 
+    temp_elements = []
+    for ele in jdata['elements']:
+        temp_elements.append(ele[0].upper() + ele[1:])
+    jdata['elements'] = temp_elements
+    print("Elements are", jdata['elements'])
 
+    ## Iteration 
     stage_list = [int(i) for i in jdata['stages']]
-
     for stage in stage_list:
         if stage == 1 :
+            print("Current stage is 1, relax")
             create_path(out_dir)
             shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
             if from_poscar :
@@ -803,13 +876,17 @@ def _main() :
                 make_super_cell(jdata)
                 place_element(jdata)
             make_vasp_relax(jdata, mdata)
+            run_vasp_relax(jdata, mdata, fp_ssh_sess)
         elif stage == 2 :
+            print("Current stage is 2, perturb and scale")
             make_scale(jdata)
             pert_scaled(jdata)
         elif stage == 3 :
+            print("Current stage is 3, run a short md")
             make_vasp_md(jdata)
-            run_vasp_md(jdata, mdata)
+            run_vasp_md(jdata, mdata, fp_ssh_sess)
         elif stage == 4 :
+            print("Current stage is 4, collect data")
             coll_vasp_md(jdata)
         else :
             raise RuntimeError("unknown stage %d" % stage)