Merge pull request #65 from kevinwenminion/devel-1.2.0

refine infomation print
deepmodeling · Apr 20, 2024 · 109af0d · 109af0d
2 parents 7dd9133 + 6652fa2
commit 109af0d
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Showing 7 changed files with 29 additions and 29 deletions.
diff --git a/apex/core/property/EOS.py b/apex/core/property/EOS.py
@@ -84,7 +84,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
         task_list = []
         if self.reprod:
-            logging.info("eos reproduce starts")
+            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"])
@@ -98,7 +98,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("eos refine starts")
+                print("eos refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -127,7 +127,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     )
 
             else:
-                logging.info(
+                print(
                     "gen eos from "
                     + str(self.vol_start)
                     + " to "
@@ -136,9 +136,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     + str(self.vol_step)
                 )
                 if self.vol_abs:
-                    logging.info("treat vol_start and vol_end as absolute volume")
+                    print("treat vol_start and vol_end as absolute volume")
                 else:
-                    logging.info("treat vol_start and vol_end as relative volume")
+                    print("treat vol_start and vol_end as relative volume")
 
                 if self.inter_param["type"] == "abacus":
                     equi_contcar = os.path.join(

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
@@ -93,7 +93,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         os.chdir(cwd)
 
         if refine:
-            logging.info("elastic refine starts")
+            print("elastic refine starts")
             task_list = make_refine(
                 self.parameter["init_from_suffix"],
                 self.parameter["output_suffix"],

diff --git a/apex/core/property/Gamma.py b/apex/core/property/Gamma.py
@@ -108,7 +108,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
 
         if self.reprod:
-            logging.info("gamma line reproduce starts")
+            print("gamma line 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"])
@@ -121,7 +121,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("gamma line refine starts")
+                print("gamma line refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -247,7 +247,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                             os.remove(jj)
                     task_list.append(output_task)
                     # print("# %03d generate " % ii, output_task)
-                    logging.info(
+                    print(
                         "# %03d generate " % count,
                         output_task,
                         " \t %d atoms" % len(obtained_slab.sites)

diff --git a/apex/core/property/Interstitial.py b/apex/core/property/Interstitial.py
@@ -91,7 +91,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
 
         if self.reprod:
-            logging.info("interstitial reproduce starts")
+            print("interstitial 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"])
@@ -105,7 +105,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("interstitial refine starts")
+                print("interstitial refine starts")
                 self.task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -173,7 +173,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 conv_ss.to("POSCAR", "POSCAR")
                 ss = conv_ss
                 if self.lattice_type:
-                    logging.info(msg=f'Adopt user indicated lattice type: {self.lattice_type}')
+                    print(f'Adopt user indicated lattice type: {self.lattice_type}')
                     self.structure_type = self.lattice_type
                 os.chdir(cwd)
 
@@ -210,7 +210,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         #            dss.append(jj.generate_defect_structure(self.supercell))
                         self.dss = dss
 
-                logging.info(
+                print(
                     "gen interstitial with supercell "
                     + str(self.supercell)
                     + " with element "
@@ -411,7 +411,7 @@ def __gen_tasks(self, interstitial_dict):
             with open("POSCAR", "w+") as fout:
                 for ii in new_pos_line:
                     print(ii, file=fout)
-            logging.info(f"gen {type_str}")
+            print(f"gen {type_str}")
             os.chdir(cwd)
 
         total_task = len(self.dss) + len(interstitial_dict)

diff --git a/apex/core/property/Phonon.py b/apex/core/property/Phonon.py
@@ -109,7 +109,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
 
         if self.reprod:
-            logging.info("phonon reproduce starts")
+            print("phonon 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"])
@@ -124,7 +124,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("phonon refine starts")
+                print("phonon refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -178,13 +178,13 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 if not self.BAND:
                     # use seekpath to get band path
                     if self.seekpath_from_original:
-                        logging.info(msg='Band path (BAND) not indicated, using seekpath from original cell')
+                        print('Band path (BAND) not indicated, using seekpath from original cell')
                         sp = seekpath.get_path_orig_cell(
                             self.get_seekpath_structure(ss),
                             **self.seekpath_param
                         )
                     else:
-                        logging.info(msg='Band path (BAND) not indicated, using seekpath for it')
+                        print('Band path (BAND) not indicated, using seekpath for it')
                         sp = seekpath.get_path(
                             self.get_seekpath_structure(ss),
                             **self.seekpath_param
@@ -193,7 +193,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     self.BAND, self.BAND_LABELS = self.band_list_2_phonopy_band_string(band_list)
                 else:
                     # use user input band path
-                    logging.info(msg=f'Band path (BAND) indicated, using: {self.BAND}')
+                    print(f'Band path (BAND) indicated, using: {self.BAND}')
                     band_list = self.phonopy_band_string_2_band_list(self.BAND, self.BAND_LABELS)
 
                 dumpfn(band_list, os.path.join(path_to_work, "band_path.json"), indent=4)
@@ -503,9 +503,9 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 os.system('phonopy -f task.0*/OUT.ABACUS/running_scf.log')
                 os.system('phonopy -f task.0*/OUT.ABACUS/running_scf.log')
                 if os.path.exists("FORCE_SETS"):
-                    logging.info('FORCE_SETS is created')
+                    print('FORCE_SETS is created')
                 else:
-                    logging.info('FORCE_SETS can not be created')
+                    logging.warning('FORCE_SETS can not be created')
                 os.system('phonopy band.conf --abacus')
                 os.system('phonopy-bandplot --gnuplot band.yaml > band.dat')
 
@@ -524,17 +524,17 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                             self.supercell_size[1],
                             self.supercell_size[2]))
                     os.system('phonopy-bandplot --gnuplot band.yaml > band.dat')
-                    logging.info('band.dat is created')
+                    print('band.dat is created')
                     shutil.copyfile("band.dat", work_path/"band.dat")
 
                 elif self.approach == "displacement":
                     shutil.copyfile("task.000000/band.conf", "band.conf")
                     shutil.copyfile("task.000000/phonopy_disp.yaml", "phonopy_disp.yaml")
                     os.system('phonopy -f task.0*/vasprun.xml')
                     if os.path.exists("FORCE_SETS"):
-                        logging.info('FORCE_SETS is created')
+                        print('FORCE_SETS is created')
                     else:
-                        logging.info('FORCE_SETS can not be created')
+                        logging.warning('FORCE_SETS can not be created')
                     os.system('phonopy --dim="%s %s %s" -c POSCAR-unitcell band.conf' % (
                         self.supercell_size[0],
                         self.supercell_size[1],

diff --git a/apex/core/property/Surface.py b/apex/core/property/Surface.py
@@ -101,7 +101,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("surface refine starts")
+                print("surface refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -174,7 +174,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         if os.path.exists(jj):
                             os.remove(jj)
                     task_list.append(output_task)
-                    logging.info(
+                    print(
                         "# %03d generate " % ii,
                         output_task,
                         " \t %d atoms" % len(all_slabs[ii].sites),

diff --git a/apex/core/property/Vacancy.py b/apex/core/property/Vacancy.py
@@ -78,7 +78,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
 
         if self.reprod:
-            logging.info("vacancy reproduce starts")
+            print("vacancy 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"])
@@ -92,7 +92,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("vacancy refine starts")
+                print("vacancy refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -142,7 +142,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         jj.get_supercell_structure(sc_mat=np.diag(self.supercell, k=0))
                     )
 
-                logging.info("gen vacancy with supercell " + str(self.supercell))
+                print("gen vacancy with supercell " + str(self.supercell))
                 os.chdir(path_to_work)
                 if os.path.exists(POSCAR):
                     os.remove(POSCAR)