Merge pull request #40 from robinzyb/devel

temporarily disable the parser for `-1.stress`

cp2kdata/output.py

@@ -382,7 +382,15 @@ def parse_md(self):
         stress_file_list = glob.glob(
             os.path.join(self.path_prefix, "*.stress"))
         if stress_file_list:
-            self.stress_tensor_list = parse_md_stress(stress_file_list[0])
+            print(
+                f"cp2kdata found a stress file: {stress_file_list[0]}"
+                "But the parser for stress is not supported yet"
+                )
+            #TODO: the unit of stress is bar in -1.stress file, but not GPa in the output file
+            #TODO: however, covert bar to GPa is not consistent with the output file!
+            #TODO: check this latter
+            #self.stress_tensor_list = parse_md_stress(stress_file_list[0])
+            self.stress_tensor_list = None
         else:
             print(
                 f"Parsing Stress from the CP2K output/log file: {self.filename}")

docs/dpdata_plugin.md

@@ -16,6 +16,22 @@ Currently, `CP2KData` supports two formats for use with `dpdata`:
    print(dp)
    ```
 
+   Recommended Setups in the input of  `ENERGY_FORCE` calculation.
+   ```shell
+   &FORCE_EVAL
+      # if stress tensor is not need to computed, comment out the below line.
+      STRESS_TENSOR ANALYTICAL
+      &PRINT
+         &FORCES ON
+         &END FORCES
+         # if stress tensor is not need to computed, comment out the below line
+         &STRESS_TENSOR ON
+         # if stress tensor is not need to computed, comment out the below line
+         &END STRESS_TENSOR
+      &END PRINT
+   &END FORCE_EVAL
+   ```
+
 2. `cp2kdata/md` format for parsing `MD` outputs.
 
    Example for parsing `MD` outputs:
@@ -27,5 +43,54 @@ Currently, `CP2KData` supports two formats for use with `dpdata`:
    dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
    print(dp)
    ```
+   Recommended Setups in the input of  `MD` calculation.
+
+   ```shell
+   @SET frequency 100
+   &FORCE_EVAL
+      # if stress tensor is not need to computed, comment out the below line.
+      STRESS_TENSOR ANALYTICAL d
+      &PRINT
+         # if stress tensor is not need to computed, comment out the below line
+         &STRESS_TENSOR ON
+         # if stress tensor is not need to computed, comment out the below line
+            &EACH
+         # if stress tensor is not need to computed, comment out the below line
+               MD ${frequency}
+         # if stress tensor is not need to computed, comment out the below line
+            &END EACH
+         # if stress tensor is not need to computed, comment out the below line
+         &END STRESS_TENSOR
+      &END PRINT
+   &END FORCE_EVAL
+   &MOTION
+      &MD
+         &PRINT
+            &ENERGY
+               &EACH
+                  MD ${frequency}
+               &END EACH
+            &END ENERGY
+         &END PRINT
+      &END MD
+      &PRINT
+         &CELL
+            &EACH
+               MD ${frequency}
+            &END EACH
+         &END CELL
+         &FORCES
+            &EACH
+               MD ${frequency}
+            &END EACH
+         &END FORCES
+         &TRAJECTORY
+            &EACH
+               MD ${frequency}
+            &END EACH
+         &END TRAJECTORY
+      &END PRINT
+   &END MOTION
+   ```
 
 These examples demonstrate how to use `Cp2kData` with `dpdata` to parse and work with data from CP2K simulations in the specified formats.

pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "Cp2kData"
-version = "0.6.4"
+version = "0.6.5"
 description = "A Small Package to Postprocess Cp2k Output"
 authors = [
     {name = "Yongbin Zhuang", email = "robinzhuang@outlook.com"}