Update shuffle_poscar feature in run.py

dpgen/generator/run.py

@@ -338,7 +338,7 @@
         and iter_index > 0
         and _check_skip_train(model_devi_jobs[iter_index - 1])
     ):
         log_task("skip training at step %d " % (iter_index - 1))  # noqa: UP031
         copy_model(numb_models, iter_index - 1, iter_index, suffix)
         return
     else:
@@ -522,7 +522,7 @@
                     1.0 - training_reuse_old_ratio,
                 )
             )
         elif Version("2") <= Version(mdata["deepmd_version"]) < Version("4"):
             jinput["training"]["training_data"]["auto_prob"] = (
                 "prob_sys_size; 0:%d:%f; %d:%d:%f"  # noqa: UP031
                 % (
@@ -953,7 +953,7 @@
         if jdata.get("dp_compress", False):
             model_name = f"frozen_model_compressed{suffix}"
 
         ofile = os.path.join(work_path, "graph.%03d%s" % (ii, suffix))  # noqa: UP031
         task_file = os.path.join(train_task_fmt % ii, model_name)
         if os.path.isfile(ofile):
             os.remove(ofile)
@@ -1239,7 +1239,7 @@
                         "%s.%03d" % (_calypso_run_opt_path, temp_idx)  # noqa: UP031
                     )
             elif not jdata.get("vsc", False):
                 calypso_run_opt_path.append("%s.%03d" % (_calypso_run_opt_path, 0))  # noqa: UP031
 
         # mode 2: control each iteration to generate structures in specific way
         # by providing model_devi_jobs key
@@ -1305,7 +1305,7 @@
                     type_map=jdata["type_map"],
                 )
                 if shuffle_poscar:
-                    system.data["coords"] = rng.permuted(system.data["coords"], axis=1)
+                    rng.shuffle(system.data["coords"], axis=1)
                 if jdata.get("model_devi_nopbc", False):
                     system.remove_pbc()
                 system.to_lammps_lmp(os.path.join(conf_path, lmp_name))
@@ -2074,7 +2074,7 @@
         grp_name = gromacs_settings.get("group_name", "Other")
         trj_freq = cur_job.get("trj_freq", 10)
 
         command = "%s grompp -f %s -p %s -c %s -o %s -maxwarn %d" % (  # noqa: UP031
             model_devi_exec,
             mdp_filename,
             topol_filename,
@@ -3323,7 +3323,7 @@
         if orb_files_stru:
             assert "fp_orb_files" in jdata, "need to define fp_orb_files in jdata"
         if descriptor_file_stru:
             assert "fp_dpks_descriptor" in jdata, (
                 "need to define fp_dpks_descriptor in jdata"
             )
 
@@ -3341,13 +3341,13 @@
                 os.symlink(src_file, pp_files_stru[idx])
             if orb_files_stru:
                 src_file = os.path.join(fp_pp_path, jdata["fp_orb_files"][type_map_idx])
                 assert os.path.isfile(src_file), (
                     f"Can not find the orbital file {src_file}"
                 )
                 os.symlink(src_file, orb_files_stru[idx])
         if descriptor_file_stru:
             src_file = os.path.join(fp_pp_path, jdata["fp_dpks_descriptor"])
             assert os.path.isfile(src_file), (
                 f"Can not find the descriptor file {src_file}"
             )
             os.symlink(src_file, descriptor_file_stru)
@@ -4295,7 +4295,7 @@
 
     if tcount == 0:
         rfail = 0.0
         dlog.info("failed frame: %6d in %6d " % (icount, tcount))  # noqa: UP031
     else:
         rfail = float(icount) / float(tcount)
         dlog.info(
@@ -4534,7 +4534,7 @@
 
     if tcount == 0:
         rfail = 0.0
         dlog.info("failed frame: %6d in %6d " % (tcount - icount, tcount))  # noqa: UP031
     else:
         rfail = float(tcount - icount) / float(tcount)
         dlog.info(
@@ -4782,7 +4782,7 @@
                 iter_rec = [int(x) for x in line.split()]
         if len(iter_rec) == 0:
             raise ValueError("There should not be blank lines in record.dpgen.")
         dlog.info("continue from iter %03d task %02d" % (iter_rec[0], iter_rec[1]))  # noqa: UP031
 
     cont = True
     ii = -1
@@ -4795,7 +4795,7 @@
         for jj in range(numb_task):
             if ii * max_tasks + jj <= iter_rec[0] * max_tasks + iter_rec[1]:
                 continue
             task_name = "task %02d" % jj  # noqa: UP031
             sepline(f"{iter_name} {task_name}", "-")
             if jj == 0:
                 log_iter("make_train", ii, jj)
@@ -4828,7 +4828,7 @@
                 log_iter("post_fp", ii, jj)
                 post_fp(ii, jdata)
             else:
                 raise RuntimeError("unknown task %d, something wrong" % jj)  # noqa: UP031
             record_iter(record, ii, jj)