dpdata_plugin.md

CP2KData Plugin for dpdata

CP2KData supports a plugin for dpdata. When you install CP2KData using pip, the plugin for dpdata is automatically installed as well.

For instructions on how to use dpdata, please refer to the official repository: https://github.com/deepmodeling/dpdata.

In the following, we provide two exmples that demonstrate how to use Cp2kData with dpdata to parse data from CP2K simulations in specified formats.

Currently, CP2KData supports two formats for use with dpdata:

1. cp2kdata/e_f format for parsing ENERGY_FORCE outputs.

   Example for parsing ENERGY_FORCE outputs:

   import dpdata
   
   dp = dpdata.LabeledSystem("cp2k_e_f_output", fmt="cp2kdata/e_f")
   print(dp)

   Recommended Setups in the input of ENERGY_FORCE calculation.

   &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

   Single-point energy calculations are usually distributed across multiple folders. We need to loop through these folders. Here, I provide a script that can perform this task.

   import dpdata
   from pathlib import Path
   
   
   system_list = [
      "system_1",
      "system_2"
   ]
   prefix_wkdir = "stc_"
   cp2k_log_name = "output"
   
   root=Path("./")
   
   # make a folder to store the datasets
   datadir=root/"data_set_new"
   datadir.mkdir(exist_ok=True, parents=True)
   
   for system in system_list:
      wkdirs = root/f"{system}"
      wkdirs = list(wkdirs.glob(f"{prefix_wkdir}*"))
      wkdirs.sort()
   
      dp = None
      for wkdir in wkdirs:
         print(f"process {wkdir}")
         if dp == None:
               dp = dpdata.LabeledSystem(wkdir/cp2k_log_name, fmt="cp2kdata/e_f")
         else:
               dp += dpdata.LabeledSystem(wkdir/cp2k_log_name, fmt="cp2kdata/e_f")
   
      dp.to_deepmd_npy(datadir/system)

2. cp2kdata/md format for parsing MD outputs.

   Example for parsing MD outputs:

   import dpdata
   
   cp2kmd_dir = "."
   cp2kmd_output_name = "output"
   dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
   print(dp)

   Recommended Setups in the input of MD calculation.

   @SET frequency 100
   &FORCE_EVAL
      # if stress tensor is not need to computed, comment out the below line.
      STRESS_TENSOR ANALYTICAL 
      &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

   In some cases, cp2k md simulations are restarted from -1.restart file in which the initial structure will not be evaluated again. Therefore, the initial cell information should not be parsed again. Otherwise, the number of frames for cells is inconsistent with those for poses, forces, and energies. Cp2kdata can automatically check whether the simulations are restarted or not through the header information of output:

    *******************************************************************************
    *                            RESTART INFORMATION                              *
    *******************************************************************************
    *                                                                             *
    *    RESTART FILE NAME: bivo4-water-1.restart                                 *
    *                                                                             *
    * RESTARTED QUANTITIES:                                                       *
    *                       CELL                                                  *
    *                       COORDINATES                                           *
    *                       RANDOM NUMBER GENERATOR                               *
    *                       VELOCITIES                                            *
    *                       MD COUNTERS                                           *
    *                       MD AVERAGES                                           *
    *                       PARTICLE THERMOSTAT                                   *
    *                       REAL TIME PROPAGATION                                 *
    *                       PINT BEAD POSITIONS                                   *
    *                       PINT BEAD VELOCITIES                                  *
    *                       PINT NOSE THERMOSTAT                                  *
    *                       PINT GLE THERMOSTAT                                   *
    *                       HELIUM BEAD POSITIONS                                 *
    *                       HELIUM PERMUTATION STATE                              *
    *                       HELIUM FORCES ON SOLUTE                               *
    *                       HELIUM RNG STATE                                      *
    *******************************************************************************
   

   if the simulations are restarted using:

   &EXT_RESTART
      RESTART_FILE_NAME Li-LiFSI-DME-1-2-1.restart
   &END EXT_RESTART
   

   In case your restarted output doesn't have the above header, you can explicitly tell the cp2kdata/dpdata by setting restart=True,

   # restart = True in case the output doesn't contains header
   dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md", restart=True)