diff --git a/_api/cp2kdata.output.html b/_api/cp2kdata.output.html index 6f05422..8401f51 100644 --- a/_api/cp2kdata.output.html +++ b/_api/cp2kdata.output.html @@ -446,9 +446,14 @@

cp2kdata.output module

static check_run_type(run_type)[source]#
+
+
+static drop_first_info(cp2k_info, array, info='info')[source]#
+
+
-static drop_last_info(cp2k_info, array)[source]#
+static drop_last_info(cp2k_info, array, info='info')[source]#
diff --git a/_api/cp2kdata.utils.html b/_api/cp2kdata.utils.html index 1d23f60..4e1caaf 100644 --- a/_api/cp2kdata.utils.html +++ b/_api/cp2kdata.utils.html @@ -477,13 +477,6 @@

cp2kdata.utils module

cp2kdata.utils.interpolate_spline(old_x, old_y, new_x)[source]#
-
-
-cp2kdata.utils.printtbox(arg)[source]#
-

This function is a print decorated with a few characters so that the -print function present a characteristic string. Useful for postprocess.

-
-
cp2kdata.utils.set_pbc(pos, cell)[source]#
diff --git a/_modules/cp2kdata/block_parser/header_info.html b/_modules/cp2kdata/block_parser/header_info.html index f864ef1..30f6b5c 100644 --- a/_modules/cp2kdata/block_parser/header_info.html +++ b/_modules/cp2kdata/block_parser/header_info.html @@ -383,7 +383,9 @@

Source code for cp2kdata.block_parser.header_info

from dataclasses import dataclass # use monty.re because it can terminate on match from monty.re import regrep +from cp2kdata.log import get_logger +logger = get_logger(__name__)
[docs]@dataclass class Cp2kInfo: @@ -424,6 +426,8 @@

Source code for cp2kdata.block_parser.header_info

raise ValueError(f"More than one restart information found in {filename}") elif num_match_restart == 1: cp2k_restart = True + logger.debug(f"Found restart information in the output header") + elif num_match_restart == 0: cp2k_restart = False diff --git a/_modules/cp2kdata/output.html b/_modules/cp2kdata/output.html index 9ec0236..594065d 100644 --- a/_modules/cp2kdata/output.html +++ b/_modules/cp2kdata/output.html @@ -480,6 +480,7 @@

Source code for cp2kdata.output

         # restart should be true or false
         if restart is not None:
             self.cp2k_info.restart = restart
+            logger.debug("Overwrite restart information with user provided restart = True.")
 
         self.check_run_type(run_type=self.global_info.run_type)
 
@@ -782,8 +783,12 @@ 
Source code for cp2kdata.output
             format_logger(info="Forces", filename=self.filename)
             self.atomic_forces_list = parse_atomic_forces_list(
                 self.output_file)
+
+            self.atomic_forces_list = self.drop_first_info(
+                self.cp2k_info, self.atomic_forces_list, info="forces")
+
             self.atomic_forces_list = self.drop_last_info(
-                self.cp2k_info, self.atomic_forces_list)
+                self.cp2k_info, self.atomic_forces_list, info="forces")
 
         stress_file_list = glob.glob(
             os.path.join(self.path_prefix, "*.stress"))
@@ -802,8 +807,13 @@ 
Source code for cp2kdata.output
             self.stress_tensor_list = parse_stress_tensor_list(
                 self.output_file)
 
-            self.stress_tensor_list = self.drop_last_info(
-                self.cp2k_info, self.stress_tensor_list)
+            # stress tensor could be None if the output file doesn't contain stress information
+            if self.stress_tensor_list is not None:
+                self.stress_tensor_list = self.drop_first_info(
+                    self.cp2k_info, self.stress_tensor_list, info="stresses")
+
+                self.stress_tensor_list = self.drop_last_info(
+                    self.cp2k_info, self.stress_tensor_list, info="stresses")
 
         self.num_frames = len(self.energies_list)
 
@@ -901,12 +911,22 @@ 
Source code for cp2kdata.output
 
[docs]    def get_vib_freq_list(self):
         return self.vib_freq_list

 
+
[docs]    @staticmethod
+    def drop_first_info(cp2k_info, array, info="info"):
+        # drop first info parsed from output if it restart from preivous MD run
+        if cp2k_info.restart == True:
+            logger.info(
+                f"The cp2k output is restarted from previous MD run, drop the first {info}."
+            )
+            array = array[1:]
+        return array

+
 
[docs]    @staticmethod
-    def drop_last_info(cp2k_info, array):
+    def drop_last_info(cp2k_info, array, info="info"):
         # drop last info parsed from output if it is terminated by request (touch EXIT)
         if cp2k_info.terminated_by_request == True:
             print(
-                "cp2kdata found the cp2k output is terminated by request, drop the last info.")
+                f"The cp2k output is terminated by user request, drop the last {info}.")
             array = array[:-1]
         return array

 
diff --git a/_modules/cp2kdata/utils.html b/_modules/cp2kdata/utils.html
index 0323800..c3fe217 100644
--- a/_modules/cp2kdata/utils.html
+++ b/_modules/cp2kdata/utils.html
@@ -459,14 +459,6 @@ 
Source code for cp2kdata.utils
         tot_gr += s_gr/frames
     return tot_gr

 
-
-
[docs]def printtbox(arg):
-    """
-    This function is a print decorated with a few characters so that the
-    print function present a characteristic string. Useful for postprocess.
-    """
-    print("--> CP2KDATA: {0}".format(arg))

-
 
[docs]def format_logger(info, filename):
     logger.debug(f"Parsing {info:10} from {filename}")

 
diff --git a/genindex.html b/genindex.html
index f6c2990..d47da02 100644
--- a/genindex.html
+++ b/genindex.html
@@ -743,6 +743,8 @@ 
D

 
   
   
@@ -1153,8 +1155,6 @@ 
P

       
  • plot_U_test() (in module cp2kdata.plots.test_plot)
 
    • 
       
  • print_level (cp2kdata.block_parser.header_info.GlobalInfo attribute)
-
    • 
-      
  • printtbox() (in module cp2kdata.utils)
 
    • 
   
 
diff --git a/objects.inv b/objects.inv
index 9a66550..14e62b1 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 87f333e..47c6031 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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