pwact 0.4.0.dev0__tar.gz → 0.4.1__tar.gz

{pwact-0.4.0.dev0 → pwact-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pwact
-Version: 0.4.0.dev0
+Version: 0.4.1
 Summary: PWACT is an open-source automated active learning platform based on MatPL for efficient data sampling.
 Home-page: https://github.com/LonxunQuantum/PWact
 Author: LonxunQuantum

{pwact-0.4.0.dev0 → pwact-0.4.1}/pwact/utils/app_lib/lammps.py

@@ -259,7 +259,7 @@ def make_lammps_input_from_lmp_in_file(
     # boundary        p p p
     # atom_style      atomic
     # remove mass pair_style pair_coeff dump
-    lmp_content = remove_lmps_lines(lmp_content)
+    lmp_content, insert_info = remove_lmps_lines(lmp_content)
     lmp_content.insert(0, "variable        DUMP_FREQ       equal %d\n" % trj_freq)
     lmp_content.insert(1, "variable        restart         equal %d\n" % restart)
     
@@ -290,10 +290,15 @@ def make_lammps_input_from_lmp_in_file(
     
     if merge_traj is True:
         dump_line = "dump            1 all custom ${DUMP_FREQ} all.lammpstrj id type x y z fx fy fz\n"
-        dump_line += 'if "${restart} > 0" then "dump_modify     1 append yes"\n'
+        if "dump_modify" in insert_info.keys():
+            dump_line += 'if "${restart} > 0" then' + 'dump_modify 1 {} append yes\n'.format(" ".join(insert_info['dump_modify'].split()[2:]))
+        else:
+            dump_line += 'if "${restart} > 0" then "dump_modify     1 append yes"\n'
     else:
         dump_line = "dump            1 all custom ${DUMP_FREQ} traj/*.lammpstrj id type x y z fx fy fz\n"
-    
+        if "dump_modify" in insert_info.keys():
+            dump_line += 'dump_modify 1 {}\n'.format(" ".join(insert_info['dump_modify'].split()[2:]))
+
     dump_line += "restart         10000 lmps.restart\n"
     dump_line += "\n"
     
@@ -307,16 +312,38 @@ def make_lammps_input_from_lmp_in_file(
     return "".join(lmp_content)
 
 def remove_lmps_lines(lmps_lines):
-    removes = ["dump_freq", "units", "boundary", "restart","atom_style", "read_data", "mass", "pair_style", "pair_coeff", "dump"]
-    new_lines = [
-        line for line in lmps_lines 
-        if line.lstrip().startswith('#')
-        or not any(
-            keyword.lower() in line.lower() 
-            for keyword in removes
-        )
-        ]
-    return new_lines
+    removes = ["dump_freq", "restart","read_data"]
+    remove_head = ["mass", "units", "boundary", "atom_style", "pair_style", "pair_coeff", "dump"]
+
+    insert_head = ["dump_modify"]
+    new_line = []
+    insert_info = {}
+    for idx, line in enumerate(lmps_lines):
+        if line.lstrip() == '' or line.lstrip().startswith('#'):
+            new_line.append(line)
+            continue
+        if any (keyword.lower() == line.lstrip().split()[0].lower() for keyword in insert_head):
+            insert_info[line.lstrip().split()[0].lower()] = line
+            continue
+        if any(
+            keyword.lower() in line.lower() for keyword in removes
+        ):
+            continue
+        if any (keyword.lower() == line.lstrip().split()[0].lower() for keyword in remove_head):
+            continue
+        new_line.append(line)
+    # new_lines = [
+    #     line for line in lmps_lines 
+    #     if line.lstrip().startswith('#')
+    #     or (not any(
+    #         keyword.lower() in line.lower() 
+    #         for keyword in removes
+    #     ) and not (
+    #         keyword.lower() in line.lstrip().split()[0].lower() 
+    #         for keyword in remove_head
+    #     ))
+    #     ]
+    return new_line, insert_info
 
 def find_first_run_cmd_line(lmps_lines):
     for i, line in enumerate(lmps_lines):
@@ -325,3 +352,27 @@ def find_first_run_cmd_line(lmps_lines):
             return -(len(lmps_lines) - i)
     return None
 
+if __name__=="__main__":
+    lmp_in_file = "/data/home/wuxingxing/datas/debugs/czy/lammps.in"
+    with open(lmp_in_file, 'r') as rf:
+        lmp_content = rf.readlines()
+    runline_idx = find_first_run_cmd_line(lmp_content)
+    if runline_idx is None:
+        raise Exception("Error! The input lmp.in file: {} is missing the 'RUN' command, please modify it!".format(lmp_in_file))
+    # remove the units boundary atom_stype lines
+    # units           metal
+    # boundary        p p p
+    # atom_style      atomic
+    # remove mass pair_style pair_coeff dump
+    lmp_content,insert_info = remove_lmps_lines(lmp_content)
+    merge_traj = False
+    if merge_traj is True:
+        dump_line = "dump            1 all custom ${DUMP_FREQ} all.lammpstrj id type x y z fx fy fz\n"
+        if "dump_modify" in insert_info.keys():
+            dump_line += 'if "${restart} > 0" then' + 'dump_modify 1 {} append yes\n'.format(" ".join(insert_info['dump_modify'].split()[2:]))
+        else:
+            dump_line += 'if "${restart} > 0" then "dump_modify     1 append yes"\n'
+    else:
+        dump_line = "dump            1 all custom ${DUMP_FREQ} traj/*.lammpstrj id type x y z fx fy fz\n"
+        if "dump_modify" in insert_info.keys():
+            dump_line += 'dump_modify 1 {}\n'.format(" ".join(insert_info['dump_modify'].split()[2:]))

{pwact-0.4.0.dev0 → pwact-0.4.1}/pwact/utils/file_operation.py

@@ -19,7 +19,7 @@ def check_model_type(model_load_path):
             raise Exception("ERROR! The input model file cannot be parsed!")
         else:
             model_type  = "NEP"
-        return model_type
+    return model_type
 
 '''
 description: 

{pwact-0.4.0.dev0 → pwact-0.4.1}/pwact.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pwact
-Version: 0.4.0.dev0
+Version: 0.4.1
 Summary: PWACT is an open-source automated active learning platform based on MatPL for efficient data sampling.
 Home-page: https://github.com/LonxunQuantum/PWact
 Author: LonxunQuantum

{pwact-0.4.0.dev0 → pwact-0.4.1}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pwact", 
-    version="0.4.0.dev",
+    version="0.4.1",
     author="LonxunQuantum",
     author_email="lonxun@pwmat.com",
     description="PWACT is an open-source automated active learning platform based on MatPL for efficient data sampling.",