Merge pull request #348 from robinzyb/devel

read the cp2k fp input file provided by user

Author: amcadmus

README.md

@@ -571,7 +571,8 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
 |**fp_params["mixingweight"]** | Float| 0.05 | Proportion a of output Density Matrix to be used for the input Density Matrix of next SCF cycle (linear mixing).
 |**fp_params["NumberPulay"]** | Integer| 5 | Controls the Pulay convergence accelerator.
 | *fp_style == cp2k*
-| **fp_params** | Dict |  |Parameters for cp2k calculation. find detail in manual.cp2k.org. only the kind section must be set before use.  we assume that you have basic knowledge for cp2k input.
+| **user_fp_params** | Dict |  |Parameters for cp2k calculation. find detail in manual.cp2k.org. only the kind section must be set before use.  we assume that you have basic knowledge for cp2k input.
+| **external_input_path** | String |  | Conflict with key:user_fp_params, use the template input provided by user, some rules should be followed, read the following text in detail.
 
 
 #### Rules for cp2k input at dictionary form
@@ -609,9 +610,54 @@ Here are examples for setting:
          }
      }
  }
+ ```
+
+#### Rules for use cp2k template input provided by user
+
+See Full example template.inp and dpgen input parameter file in 
+
+`tests/generator/cp2k_make_fp_files/exinput/template.inp` and `tests/generator/param-mgo-cp2k-exinput.json` 
+
+Here is example for provide external input
+
+```python
+    {
+    "_comment":     " 02.fp ",
+     "fp_style":     "cp2k",
+     "shuffle_poscar":   false,
+     "fp_task_max":  100,
+     "fp_task_min":  10,
+     "fp_pp_path":   ".",
+     "fp_pp_files":  [],
+     "external_input_path": "./cp2k_make_fp_files/exinput/template.inp",
+     "_comment":     " that's all 
+     }
 ```
 
+the following essential section should be provided in user template
 
+```
+
+ &FORCE_EVAL
+   # add this line if you need to fit virial
+   STRESS_TENSOR ANALYTICAL
+   &PRINT
+     &FORCES ON
+     &END FORCES
+     # add this line if you need to fit virial
+     &STRESS_TENSOR ON
+     &END FORCES
+   &END PRINT
+   &SUBSYS
+     &CELL
+       ABC LEFT FOR DPGEN
+     &END CELL
+     &COORD
+     @include coord.xyz
+     &END COORD
+   &END SUBSYS
+&END FORCE_EVAL
+```
 
 ## Test: Auto-test for Deep Generator
 ###  configure and param.json

dpgen/generator/lib/cp2k.py

@@ -183,4 +183,35 @@ def make_cp2k_xyz(sys_data):
 
 
 
+def make_cp2k_input_from_external(sys_data, exinput_path):
+    # read the input content as string
+    with open(exinput_path, 'r') as f:
+        exinput = f.readlines()
+
+    # find the ABC cell string
+    for line_idx, line in enumerate(exinput):
+        if 'ABC' in line:
+            delete_cell_idx = line_idx
+            delete_cell_line = line
+
+    # remove the useless CELL line
+    exinput.remove(delete_cell_line)
+
+    # insert the cell information
+    # covert cell to cell string
+    cell = sys_data['cells'][0]
+    cell = np.reshape(cell, [3,3])
+    cell_a = np.array2string(cell[0,:])
+    cell_a = cell_a[1:-1]
+    cell_b = np.array2string(cell[1,:])
+    cell_b = cell_b[1:-1]
+    cell_c = np.array2string(cell[2,:])
+    cell_c = cell_c[1:-1]
+
+    exinput.insert(delete_cell_idx, 'A  ' + cell_a + '\n')
+    exinput.insert(delete_cell_idx+1, 'B  ' + cell_b + '\n')
+    exinput.insert(delete_cell_idx+2, 'C  ' + cell_c + '\n')
+
+    return ''.join(exinput)
+