Merge branch 'devel' into simplify_example

dpgen/generator/arginfo.py

@@ -348,12 +348,15 @@ def fp_style_siesta_args() -> List[Argument]:
 def fp_style_cp2k_args() -> List[Argument]:
     doc_user_fp_params = '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.'
     doc_external_input_path = 'Conflict with key:user_fp_params, use the template input provided by user, some rules should be followed, read the following text in detail.'
+    doc_ratio_failed = 'Check the ratio of unsuccessfully terminated jobs. If too many FP tasks are not converged, RuntimeError will be raised.'
 
     return [
-        Argument("user_fp_params", dict, optional=False,
+        Argument("user_fp_params", dict, optional=True,
                  doc=doc_user_fp_params),
-        Argument("external_input_path", str, optional=False,
+        Argument("external_input_path", str, optional=True,
                  doc=doc_external_input_path),
+        Argument("ratio_failed", float, optional=True,
+                 doc=doc_ratio_failed),
     ]
 
 

dpgen/generator/run.py

@@ -2905,7 +2905,7 @@ def make_fp (iter_index,
         make_fp_vasp(iter_index, jdata)
     elif fp_style == "pwscf" :
         make_fp_pwscf(iter_index, jdata)
-    elif fp_style == "abacus/scf" :
+    elif fp_style == "abacus" :
         make_fp_abacus_scf(iter_index, jdata)
     elif fp_style == "siesta" :
         make_fp_siesta(iter_index, jdata)
@@ -3109,7 +3109,7 @@ def run_fp (iter_index,
         forward_files = ['input'] + fp_pp_files
         backward_files = ['output']
         run_fp_inner(iter_index, jdata, mdata,  forward_files, backward_files, _qe_check_fin, log_file = 'output')
-    elif fp_style == "abacus/scf":
+    elif fp_style == "abacus":
         fp_params = {}
         if 'user_fp_params' in jdata.keys() :
             fp_params = jdata['user_fp_params']
@@ -3608,7 +3608,7 @@ def post_fp (iter_index,
         post_fp_vasp(iter_index, jdata)
     elif fp_style == "pwscf" :
         post_fp_pwscf(iter_index, jdata)
-    elif fp_style == "abacus/scf":
+    elif fp_style == "abacus":
         post_fp_abacus_scf(iter_index, jdata)
     elif fp_style == "siesta":
         post_fp_siesta(iter_index, jdata)

examples/init/abacus/fcc-Al-lcao/Al.STRU

@@ -0,0 +1,23 @@
+ATOMIC_SPECIES
+Al 26.982 Al_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+Al_gga_9au_100Ry_4s4p1d.orb
+
+LATTICE_CONSTANT
+1.8897261254578281
+
+LATTICE_VECTORS
+4.04 0.0 0.0 
+0.0 4.04 0.0 
+0.0 0.0 4.04
+
+ATOMIC_POSITIONS
+Direct    # Cartesian(Unit is LATTICE_CONSTANT)
+Al
+0.0
+4
+0.00 0.00 0.00 1 1 1
+0.51 0.51 0.00 1 1 1
+0.50 0.00 0.50 1 1 1
+0.00 0.50 0.50 1 1 1

examples/init/abacus/fcc-Al-lcao/INPUT.md

@@ -0,0 +1,28 @@
+INPUT_PARAMETERS
+#Parameters (1.General)
+suffix			ABACUS
+calculation             md
+ntype			1
+symmetry		0
+
+#Parameters (2.Iteration)
+ecutwfc			100
+scf_thr			1e-8
+scf_nmax		100
+#Parameters (3.Basis)
+basis_type		lcao
+
+#Parameters (4.Smearing)
+smearing_method		gauss
+smearing_sigma			0.002
+
+#Parameters (5.Mixing)
+mixing_type		pulay
+mixing_beta		0.3
+
+cal_stress 1
+
+md_type 	0
+md_nstep        10
+md_tfirst 10
+md_tfreq        0.5

examples/init/abacus/fcc-Al-lcao/INPUT.rlx

@@ -0,0 +1,25 @@
+INPUT_PARAMETERS
+#Parameters (1.General)
+suffix		ABACUS
+calculation     relax
+ntype		1
+symmetry	0
+
+#Parameters (2.Iteration)
+ecutwfc		100
+scf_thr		1e-8
+scf_nmax	100
+#Parameters (3.Basis)
+basis_type	lcao
+
+#Parameters (4.Smearing)
+smearing_method		gauss
+smearing_sigma		0.002
+
+#Parameters (5.Mixing)
+mixing_type		pulay
+mixing_beta		0.3
+
+cal_stress 1
+
+kspacing 100

examples/init/abacus/fcc-Al-lcao/KPT.md

@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0

examples/init/abacus/fcc-Al-lcao/KPT.rlx

@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+2 2 2 0 0 0

examples/init/abacus/fcc-Al-lcao/init.json

@@ -0,0 +1,24 @@
+{
+    "init_fp_style":    "ABACUS",
+    "stages":           [1,2,3,4],
+    "cell_type":	"diamond",
+    "super_cell":	[2, 1, 1],
+    "elements":		["Al"],
+    "from_poscar":	true,
+    "from_poscar_path":	"./Al.STRU",
+    "potcars":		["Al_ONCV_PBE-1.0.upf"], 
+    "orb_files":	["Al_gga_9au_100Ry_4s4p1d.orb"],
+    "relax_incar": 	"./INPUT.rlx",
+    "md_incar" : 	"./INPUT.md",
+    "relax_kpt":  	"./KPT.rlx",
+    "md_kpt":     	"./KPT.md",
+    "md_nstep":         3,
+    "scale":		[1.00],
+    "skip_relax":	false,
+    "pert_numb":	2,
+    "pert_box":		0.03,
+    "pert_atom":	0.01,
+    "deepgen_templ":	"../generator/template/",
+    "coll_ndata":	5000,
+    "_comment":		"that's all"
+}

examples/init/abacus/fcc-Al-lcao/machine.json

@@ -0,0 +1,106 @@
+{
+  "api_version": "1.0",
+  "deepmd_version": "2.0.1",
+  "train" :[
+    {
+      "command": "dp",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "",
+          "password": "",
+          "program_id": ,
+            "keep_backup":true,
+            "input_data":{
+                "job_type": "indicate",
+                "log_file": "00*/train.log",
+                "grouped":true,
+                "job_name": "dpgen_train_job",
+                "disk_size": 200,
+                "scass_type":"",
+                "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"],
+                "checkpoint_time":30,
+                "platform": "",
+		"region":"",
+                "image_name":"",
+                "on_demand":0,
+                "job_type":""
+            }
+        }
+      },
+      "resources": {
+        "local_root":"./",
+        "group_size": 1
+      }
+    }],
+  "model_devi":
+    [{
+      "command": "lmp -i input.lammps -v restart 0",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "",
+          "password": "",
+          "program_id": ,
+            "keep_backup":true,
+            "input_data":{
+              "job_type": "indicate",
+              "log_file": "*/model_devi.log",
+              "grouped":true,
+              "job_name": "dpgen_model_devi_job",
+              "disk_size": 200,
+              "scass_type":"",
+              "platform": "",
+		"region":"",
+              "image_name":"",
+              "checkpoint_files": "sync_files",
+              "checkpoint_time":30,
+              "on_demand":0,
+	      "job_type":""
+            }
+        }
+      },
+      "resources": {
+        "local_root":"./",
+        "group_size": 50
+      }
+    }],
+  "fp":
+    [{
+      "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "",
+          "password": "",
+          "program_id": ,
+            "keep_backup":true,
+            "input_data":{
+              "job_type": "indicate",
+              "log_file": "task*/fp.log",
+              "grouped":true,
+              "job_name": "dpgen_fp_job",
+              "disk_size": 100,
+              "checkpoint_files": "sync_files",
+              "checkpoint_time":30,
+              "scass_type":"",
+              "platform": "",
+              "image_name":"",
+              "on_demand":0
+            }
+        }
+      },
+      "resources": {
+        "group_size": 50,
+        "local_root":"./",
+        "source_list": [""]
+      }
+    }
+  ]
+}

examples/init/abacus/fcc-Al-pw/Al.STRU

@@ -0,0 +1,20 @@
+ATOMIC_SPECIES
+Al 26.982 Al_ONCV_PBE-1.0.upf
+
+LATTICE_CONSTANT
+1.8897261254578281
+
+LATTICE_VECTORS
+4.04 0.0 0.0 
+0.0 4.04 0.0 
+0.0 0.0 4.04
+
+ATOMIC_POSITIONS
+Direct    # Cartesian(Unit is LATTICE_CONSTANT)
+Al
+0.0
+4
+0.00 0.00 0.00 1 1 1
+0.48 0.53 0.00 1 1 1
+0.50 0.00 0.50 1 1 1
+0.00 0.50 0.50 1 1 1