Merge pull request #185 from amcadmus/devel

following the symlinks to find system dirs

Author: amcadmus

source/train/common.py

@@ -1,4 +1,4 @@
-import warnings
+import os,warnings,fnmatch
 import numpy as np
 from deepmd.env import tf
 
@@ -152,3 +152,9 @@ def get_activation_func(activation_fn):
         raise RuntimeError(activation_fn+" is not a valid activation function")
     return activation_fn_dict[activation_fn]
 
+def expand_sys_str(root_dir):
+    matches = []
+    for root, dirnames, filenames in os.walk(root_dir, followlinks=True):
+        for filename in fnmatch.filter(filenames, 'type.raw'):
+            matches.append(root)
+    return matches

source/train/test.py

@@ -7,6 +7,7 @@
 import numpy as np
 
 from deepmd.Data import DeepmdData
+from deepmd.common import expand_sys_str
 from deepmd import DeepEval
 from deepmd import DeepPot
 from deepmd import DeepDipole
@@ -16,10 +17,7 @@
 
 def test (args):
     de = DeepEval(args.model)
-    all_sys = []
-    from pathlib import Path
-    for filename in Path(args.system).rglob('type.raw'):
-        all_sys.append(os.path.dirname(filename))
+    all_sys = expand_sys_str(args.system)
     for ii in all_sys:
         args.system = ii
         print ("# ---------------output of dp test--------------- ")

source/train/train.py

@@ -10,7 +10,7 @@
 from deepmd.RunOptions import RunOptions
 from deepmd.DataSystem import DeepmdDataSystem
 from deepmd.Trainer import NNPTrainer
-from deepmd.common import data_requirement
+from deepmd.common import data_requirement, expand_sys_str
 from deepmd.DataModifier import DipoleChargeModifier
 
 def create_done_queue(cluster_spec, task_index):
@@ -80,13 +80,6 @@ def train (args) :
         # serial training
         _do_work(jdata, run_opt)
 
-def expand_sys_str(root_dir):
-    all_sys = []
-    from pathlib import Path
-    for filename in Path(root_dir).rglob('type.raw'):
-        all_sys.append(os.path.dirname(filename))
-    return all_sys
-
 def _do_work(jdata, run_opt):
     # init the model
     model = NNPTrainer (jdata, run_opt = run_opt)