Merge pull request #690 from amcadmus/master

merge devel branch into master

Author: amcadmus

.github/workflows/release.yml

@@ -32,3 +32,7 @@ jobs:
         repository: ${{ env.GITHUB_REPOSITORY }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  release-to-pypi:
+    uses: deepmodeling/workflows/.github/workflows/release-to-pypi.yml@main
+    secrets:
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

README.md

@@ -189,6 +189,10 @@ If you want to specify a structure as starting point for `init_bulk`, you may se
 "from_poscar":	true,
 "from_poscar_path":	"....../C_mp-47_conventional.POSCAR",
 ```
+`init_bulk` support both VASP and ABACUS for first-principle calculation. You can choose the software by specifying the key `init_fp_style`. If `init_fp_style` is not specified, the default software will be VASP. 
+
+When using ABACUS for `init_fp_style`, the keys of the paths of `INPUT` files for relaxation and MD simulations are the same as `INCAR` for VASP, which are `relax_incar` and `md_incar` respectively. You have to additionally specify `relax_kspacing` and `md_kspacing` for k points spacing, and dpgen will automatically generate `KPT` files according to them. You may also use `relax_kpt` and `md_kpt` instead of them for the relative path for `KPT` files of relaxation and MD simulations. However, either `relax_kspacing` and `md_kspacing`, or `relax_kpt` and `md_kpt` is needed. If `from_poscar` is set to `false`, you have to specify `atom_masses` in the same order as `elements`.
+
 The following table gives explicit descriptions on keys in `PARAM`.
 
 The bold notation of key (such as **Elements**) means that it's a necessary key.
@@ -200,9 +204,9 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
 |  cell_type | String  | "hcp" | Specifying which typical structure to be generated. **Options** include fcc, hcp, bcc, sc, diamond.
 | latt | Float | 4.479 | Lattice constant for single cell.
 | from_poscar | Boolean | True | Deciding whether to use a given poscar as the beginning of relaxation. If it's true, keys (`cell_type`, `latt`) will be aborted. Otherwise, these two keys are **necessary**.
-| from_poscar_path | String | "....../C_mp-47_conventional.POSCAR" | Path of POSCAR. **Necessary** if `from_poscar` is true.
-| relax_incar | String | "....../INCAR" | Path of INCAR for relaxation in VASP. **Necessary** if `stages` include 1.
-| md_incar | String |  "....../INCAR" | Path of INCAR for MD in VASP. **Necessary** if `stages` include 3.|
+| from_poscar_path | String | "....../C_mp-47_conventional.POSCAR" | Path of POSCAR for VASP or STRU for ABACUS. **Necessary** if `from_poscar` is true.
+| relax_incar | String | "....../INCAR" | Path of INCAR for VASP or INPUT for ABACUS for relaxation in VASP. **Necessary** if `stages` include 1.
+| md_incar | String |  "....../INCAR" | Path of INCAR for VASP or INPUT for ABACUS for MD in VASP. **Necessary** if `stages` include 3.|
 | **scale** | List of float | [0.980, 1.000, 1.020] | Scales for transforming cells.
 | **skip_relax** | Boolean | False | If it's true, you may directly run stage 2 (pertub and scale) using an unrelaxed POSCAR.
 | **pert_numb** | Integer | 30 | Number of pertubations for each POSCAR.
@@ -211,6 +215,12 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
 | **md_nstep** | Integer | 10 | Steps of AIMD in stage 3. If it's not equal to settings via `NSW` in `md_incar`, DP-GEN will follow `NSW`.
 | **coll_ndata** | Integer | 5000 | Maximal number of collected data.
 | type_map | List | [ "Mg", "Al"] | The indices of elements in deepmd formats will be set in this order.
+| init_fp_style | String | "ABACUS" or "VASP" | First-principle software. If this key is abscent, the default value will be "VASP".
+| relax_kpt | String | "....../KPT" | Path of `KPT` file for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS".
+| relax_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS".
+| md_kpt | String | "....../KPT" | Path of `KPT` file for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS".
+| md_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS".
+| atom_masses | List of float | [24] | List of atomic masses of elements. The order should be the same as `Elements`. Only useful if `init_fp_style` is "ABACUS".
 
 ### Init_surf
 

doc/conf.py

@@ -38,6 +38,7 @@
 # ]
 
 extensions = [
+    'deepmodeling_sphinx',
     "sphinx_rtd_theme",
     'myst_parser',
     'sphinx.ext.autosummary',

doc/requirements.txt

@@ -3,3 +3,4 @@ recommonmark==0.7.1
 sphinx_rtd_theme==0.5.2
 sphinx_markdown_tables==0.0.15
 myst-parser==0.13.7
+deepmodeling_sphinx

dpgen/auto_test/EOS.py

@@ -169,8 +169,8 @@ def _compute_lower(self,
                 # 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'].sum()
-                ptr_data += '%7.3f  %8.4f \n' % (vol, task_result['energies'][-1] / task_result['atom_numbs'].sum())
+                res_data[vol] = task_result['energies'][-1] / sum(task_result['atom_numbs'])
+                ptr_data += '%7.3f  %8.4f \n' % (vol, task_result['energies'][-1] / sum(task_result['atom_numbs']))
                 # 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']))
 

dpgen/auto_test/common_equi.py

@@ -114,46 +114,6 @@ def make_equi(confs,
         inter.make_input_file(ii, 'relaxation', relax_param)
 
 
-def worker(work_path,
-           run_task,
-           forward_common_files,
-           forward_files,
-           backward_files,
-           mdata,
-           inter_type):
-    machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
-    disp = make_dispatcher(machine, resources, work_path, [run_task], group_size)
-    print("%s --> Runing... " % (work_path))
-
-    api_version = mdata.get('api_version', '0.9')
-    if LooseVersion(api_version) < LooseVersion('1.0'):
-        warnings.warn(f"the dpdispatcher will be updated to new version."
-                      f"And the interface may be changed. Please check the documents for more details")
-        disp.run_jobs(resources,
-                      command,
-                      work_path,
-                      [run_task],
-                      group_size,
-                      forward_common_files,
-                      forward_files,
-                      backward_files,
-                      outlog='outlog',
-                      errlog='errlog')
-    elif LooseVersion(api_version) >= LooseVersion('1.0'):
-        submission = make_submission(
-            mdata_machine=machine,
-            mdata_resources=resources,
-            commands=[command],
-            work_path=work_path,
-            run_tasks=run_task,
-            group_size=group_size,
-            forward_common_files=forward_common_files,
-            forward_files=forward_files,
-            backward_files=backward_files,
-            outlog='outlog',
-            errlog='errlog'
-        )
-        submission.run_submission()
 
 def run_equi(confs,
              inter_param,
@@ -166,18 +126,16 @@ def run_equi(confs,
     conf_dirs.sort()
 
     processes = len(conf_dirs)
-    pool = Pool(processes=processes)
-    print("Submit job via %d processes" % processes)
 
     # generate a list of task names like mp-xxx/relaxation/relax_task
     # ...
     work_path_list = []
     for ii in conf_dirs:
-        work_path_list.append(os.path.abspath(os.path.join(ii, 'relaxation')))
+        work_path_list.append(os.path.join(ii, 'relaxation'))
     all_task = []
     for ii in work_path_list:
         all_task.append(os.path.join(ii, 'relax_task'))
-
+    run_tasks = all_task
     inter_type = inter_param['type']
     # vasp
     if inter_type == "vasp":
@@ -186,41 +144,51 @@ def run_equi(confs,
         mdata = convert_mdata(mdata, ["model_devi"])
     else:
         raise RuntimeError("unknown task %s, something wrong" % inter_type)
-
+    
     # dispatch the tasks
     # POSCAR here is useless
     virtual_calculator = make_calculator(inter_param, "POSCAR")
     forward_files = virtual_calculator.forward_files()
     forward_common_files = virtual_calculator.forward_common_files()
     backward_files = virtual_calculator.backward_files()
     #    backward_files += logs
-    # ...
-    run_tasks = util.collect_task(all_task, inter_type)
-    if len(run_tasks) == 0:
-        return
-    else:
-        run_tasks = [os.path.basename(ii) for ii in all_task]
-        machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
-        print('%d tasks will be submited '%len(run_tasks))
-        multiple_ret = []
-        for ii in range(len(work_path_list)):
-            work_path = work_path_list[ii]
-
-            ret = pool.apply_async(worker, (work_path,
-                                            run_tasks[ii],
-                                            forward_common_files,
-                                            forward_files,
-                                            backward_files,
-                                            mdata,
-                                            inter_type,
-                                            ))
-            multiple_ret.append(ret)
-        pool.close()
-        pool.join()
-        for ii in range(len(multiple_ret)):
-            if not multiple_ret[ii].successful():
-                raise RuntimeError("Task %d is not successful! work_path: %s " % (ii, work_path_list[ii]))
-        print('finished')
+    machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
+    work_path = os.getcwd()
+    print("%s --> Runing... " % (work_path))
+
+    api_version = mdata.get('api_version', '0.9')
+    if LooseVersion(api_version) < LooseVersion('1.0'):
+        warnings.warn(f"the dpdispatcher will be updated to new version."
+                      f"And the interface may be changed. Please check the documents for more details")
+        disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
+        disp.run_jobs(resources,
+                      command,
+                      work_path,
+                      run_tasks,
+                      group_size,
+                      forward_common_files,
+                      forward_files,
+                      backward_files,
+                      outlog='outlog',
+                      errlog='errlog')
+    elif LooseVersion(api_version) >= LooseVersion('1.0'):
+    
+        submission = make_submission(
+            mdata_machine=machine,
+            mdata_resources=resources,
+            commands=[command],
+            work_path=work_path,
+            run_tasks=run_tasks,
+            group_size=group_size,
+            forward_common_files=forward_common_files,
+            forward_files=forward_files,
+            backward_files=backward_files,
+            outlog='outlog',
+            errlog='errlog'
+        )
+        submission.run_submission()
+    
+    
 
 def post_equi(confs, inter_param):
     # find all POSCARs and their name like mp-xxx

dpgen/auto_test/common_prop.py

@@ -173,6 +173,7 @@ def run_property(confs,
     pool.join()
     for ii in range(len(multiple_ret)):
         if not multiple_ret[ii].successful():
+            print("ERROR:", multiple_ret[ii].get())
             raise RuntimeError("Job %d is not successful!" % ii)
     print('%d jobs are finished' % len(multiple_ret))
 
@@ -186,11 +187,11 @@ def worker(work_path,
            inter_type):
     run_tasks = [os.path.basename(ii) for ii in all_task]
     machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
-    disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
     api_version = mdata.get('api_version', '0.9')
     if LooseVersion(api_version) < LooseVersion('1.0'):
         warnings.warn(f"the dpdispatcher will be updated to new version."
             f"And the interface may be changed. Please check the documents for more details")
+        disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
         disp.run_jobs(resources,
                   command,
                   work_path,

dpgen/auto_test/lib/lammps.py

@@ -241,6 +241,8 @@ def make_lammps_equi(conf, type_map, interaction, param,
         ret += "fix             1 all box/relax iso 0.0 \n"
         ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
         ret += "fix             1 all box/relax aniso 0.0 \n"
+        ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+        ret += "fix             1 all box/relax tri 0.0 \n"
     ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
     ret += "variable        N equal count(all)\n"
     ret += "variable        V equal vol\n"