Merge pull request #353 from deepmodeling/devel

merge recent development on devel to master

Author: amcadmus

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+name: Python package
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8]
+        PYMATGEN_VERSION: [2019.1.13, 2019.7.30]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: pip install coverage codecov pymatgen==${{ matrix.PYMATGEN_VERSION }} .
+    - name: Test
+      run: coverage run --source=./dpgen -m unittest -v && coverage report
+    - run: codecov

.gitignore

@@ -37,4 +37,5 @@ dpgen.egg-info
 .eggs
 .coverage
 dbconfig.json
-.vscode/*
+.vscode/*
+.idea/*

.travis.yml

@@ -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

README.md

@@ -8,7 +8,7 @@
 SHORT_CMD="dpgen"
 dlog = logging.getLogger(__name__)
 dlog.setLevel(logging.INFO)
-dlogf = logging.FileHandler(os.getcwd()+os.sep+SHORT_CMD+'.log')
+dlogf = logging.FileHandler(os.getcwd()+os.sep+SHORT_CMD+'.log', delay=True)
 dlogf_formatter=logging.Formatter('%(asctime)s - %(levelname)s : %(message)s')
 #dlogf_formatter=logging.Formatter('%(asctime)s - %(name)s - [%(filename)s:%(funcName)s - %(lineno)d ] - %(levelname)s \n %(message)s')
 dlogf.setFormatter(dlogf_formatter)

dpgen/__init__.py

@@ -0,0 +1,187 @@
+import glob
+import json
+import os
+import re
+
+import numpy as np
+from monty.serialization import loadfn, dumpfn
+
+import dpgen.auto_test.lib.vasp as vasp
+from dpgen import dlog
+from dpgen.auto_test.Property import Property
+from dpgen.auto_test.refine import make_refine
+from dpgen.auto_test.reproduce import make_repro
+from dpgen.auto_test.reproduce import post_repro
+
+
+class EOS(Property):
+    def __init__(self,
+                 parameter):
+        parameter['reproduce'] = parameter.get('reproduce', False)
+        self.reprod = parameter['reproduce']
+        if not self.reprod:
+            if not ('init_from_suffix' in parameter and 'output_suffix' in parameter):
+                self.vol_start = parameter['vol_start']
+                self.vol_end = parameter['vol_end']
+                self.vol_step = parameter['vol_step']
+            parameter['cal_type'] = parameter.get('cal_type', 'relaxation')
+            self.cal_type = parameter['cal_type']
+            default_cal_setting = {"relax_pos": True,
+                                   "relax_shape": True,
+                                   "relax_vol": False}
+            if 'cal_setting' not in parameter:
+                parameter['cal_setting'] = default_cal_setting
+            else:
+                if "relax_pos" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_pos'] = default_cal_setting['relax_pos']
+                if "relax_shape" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_shape'] = default_cal_setting['relax_shape']
+                if "relax_vol" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_vol'] = default_cal_setting['relax_vol']
+            self.cal_setting = parameter['cal_setting']
+        else:
+            parameter['cal_type'] = 'static'
+            self.cal_type = parameter['cal_type']
+            default_cal_setting = {"relax_pos": False,
+                                   "relax_shape": False,
+                                   "relax_vol": False}
+            if 'cal_setting' not in parameter:
+                parameter['cal_setting'] = default_cal_setting
+            else:
+                if "relax_pos" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_pos'] = default_cal_setting['relax_pos']
+                if "relax_shape" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_shape'] = default_cal_setting['relax_shape']
+                if "relax_vol" not in parameter['cal_setting']:
+                    parameter['cal_setting']['relax_vol'] = default_cal_setting['relax_vol']
+            self.cal_setting = parameter['cal_setting']
+            parameter['init_from_suffix'] = parameter.get('init_from_suffix', '00')
+            self.init_from_suffix = parameter['init_from_suffix']
+        self.parameter = parameter
+
+    def make_confs(self,
+                   path_to_work,
+                   path_to_equi,
+                   refine=False):
+        path_to_work = os.path.abspath(path_to_work)
+        if os.path.exists(path_to_work):
+            dlog.warning('%s already exists' % path_to_work)
+        else:
+            os.makedirs(path_to_work)
+        path_to_equi = os.path.abspath(path_to_equi)
+
+        if 'start_confs_path' in self.parameter and os.path.exists(self.parameter['start_confs_path']):
+            init_path_list = glob.glob(os.path.join(self.parameter['start_confs_path'], '*'))
+            struct_init_name_list = []
+            for ii in init_path_list:
+                struct_init_name_list.append(ii.split('/')[-1])
+            struct_output_name = path_to_work.split('/')[-2]
+            assert struct_output_name in struct_init_name_list
+            path_to_equi = os.path.abspath(os.path.join(self.parameter['start_confs_path'],
+                                                        struct_output_name, 'relaxation', 'relax_task'))
+
+        cwd = os.getcwd()
+        task_list = []
+        if self.reprod:
+            print('eos reproduce starts')
+            if 'init_data_path' not in self.parameter:
+                raise RuntimeError("please provide the initial data path to reproduce")
+            init_data_path = os.path.abspath(self.parameter['init_data_path'])
+            task_list = make_repro(init_data_path, self.init_from_suffix,
+                                   path_to_work, self.parameter.get('reprod_last_frame', True))
+            os.chdir(cwd)
+
+        else:
+            if refine:
+                print('eos refine starts')
+                task_list = make_refine(self.parameter['init_from_suffix'],
+                                        self.parameter['output_suffix'],
+                                        path_to_work)
+                os.chdir(cwd)
+
+                init_from_path = re.sub(self.parameter['output_suffix'][::-1],
+                                        self.parameter['init_from_suffix'][::-1],
+                                        path_to_work[::-1], count=1)[::-1]
+                task_list_basename = list(map(os.path.basename, task_list))
+
+                for ii in task_list_basename:
+                    init_from_task = os.path.join(init_from_path, ii)
+                    output_task = os.path.join(path_to_work, ii)
+                    os.chdir(output_task)
+                    if os.path.isfile('eos.json'):
+                        os.remove('eos.json')
+                    if os.path.islink('eos.json'):
+                        os.remove('eos.json')
+                    os.symlink(os.path.relpath(os.path.join(init_from_task, 'eos.json')), 'eos.json')
+                os.chdir(cwd)
+
+            else:
+                print('gen eos from ' + str(self.vol_start) + ' to ' + str(self.vol_end) + ' by every ' + str(self.vol_step))
+                equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
+                if not os.path.exists(equi_contcar):
+                    raise RuntimeError("please do relaxation first")
+                vol_to_poscar = vasp.poscar_vol(equi_contcar) / vasp.poscar_natoms(equi_contcar)
+                self.parameter['scale2equi'] = []
+
+                task_num = 0
+                while self.vol_start + self.vol_step * task_num < self.vol_end:
+                # for vol in np.arange(int(self.vol_start * 100), int(self.vol_end * 100), int(self.vol_step * 100)):
+                    # vol = vol / 100.0
+                    vol = self.vol_start + task_num * self.vol_step
+                    #task_num = int((vol - self.vol_start) / self.vol_step)
+                    output_task = os.path.join(path_to_work, 'task.%06d' % task_num)
+                    os.makedirs(output_task, exist_ok=True)
+                    os.chdir(output_task)
+                    for ii in ['INCAR', 'POTCAR', 'POSCAR.orig', 'POSCAR', 'conf.lmp', 'in.lammps']:
+                        if os.path.exists(ii):
+                            os.remove(ii)
+                    task_list.append(output_task)
+                    os.symlink(os.path.relpath(equi_contcar), 'POSCAR.orig')
+                    # scale = (vol / vol_to_poscar) ** (1. / 3.)
+                    scale = vol ** (1. / 3.)
+                    eos_params = {'volume': vol * vol_to_poscar, 'scale': scale}
+                    dumpfn(eos_params, 'eos.json', indent=4)
+                    self.parameter['scale2equi'].append(scale)  # 06/22
+                    vasp.poscar_scale('POSCAR.orig', 'POSCAR', scale)
+                    task_num += 1
+                os.chdir(cwd)
+        return task_list
+
+    def post_process(self, task_list):
+        pass
+
+    def task_type(self):
+        return self.parameter['type']
+
+    def task_param(self):
+        return self.parameter
+
+    def _compute_lower(self,
+                       output_file,
+                       all_tasks,
+                       all_res):
+        output_file = os.path.abspath(output_file)
+        res_data = {}
+        ptr_data = "conf_dir: " + os.path.dirname(output_file) + "\n"
+        if not self.reprod:
+            ptr_data += ' VpA(A^3)  EpA(eV)\n'
+            for ii in range(len(all_tasks)):
+                # vol = self.vol_start + ii * self.vol_step
+                vol = loadfn(os.path.join(all_tasks[ii], 'eos.json'))['volume']
+                task_result = loadfn(all_res[ii])
+                res_data[vol] = task_result['energies'][-1] / task_result['atom_numbs'][0]
+                ptr_data += '%7.3f  %8.4f \n' % (vol, task_result['energies'][-1] / task_result['atom_numbs'][0])
+                # res_data[vol] = all_res[ii]['energy'] / len(all_res[ii]['force'])
+                # ptr_data += '%7.3f  %8.4f \n' % (vol, all_res[ii]['energy'] / len(all_res[ii]['force']))
+
+        else:
+            if 'init_data_path' not in self.parameter:
+                raise RuntimeError("please provide the initial data path to reproduce")
+            init_data_path = os.path.abspath(self.parameter['init_data_path'])
+            res_data, ptr_data = post_repro(init_data_path, self.parameter['init_from_suffix'],
+                                            all_tasks, ptr_data, self.parameter.get('reprod_last_frame', True))
+
+        with open(output_file, 'w') as fp:
+            json.dump(res_data, fp, indent=4)
+
+        return res_data, ptr_data