make more examples pass argument tests (#870)

* make more examples pass argument tests * fix kspace
deepmodeling · Aug 17, 2022 · d55d400 · d55d400
1 parent 0a197f2
commit d55d400
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Showing 6 changed files with 22 additions and 27 deletions.
diff --git a/dpgen/generator/arginfo.py b/dpgen/generator/arginfo.py
@@ -46,7 +46,7 @@ def data_args() -> List[Argument]:
         Argument("init_data_sys", list,
                  optional=False, doc=doc_init_data_sys),
         Argument("sys_format", str, optional=True, default='vasp/poscar', doc=doc_sys_format),
-        Argument("init_batch_size", str, optional=True,
+        Argument("init_batch_size", [list, str], optional=True,
                  doc=doc_init_batch_size),
         Argument("sys_configs_prefix", str, optional=True,
                  doc=doc_sys_configs_prefix),
@@ -105,7 +105,7 @@ def model_devi_jobs_args() -> List[Argument]:
     # this may be not correct
     doc_sys_idx = 'Systems to be selected as the initial structure of MD and be explored. The index corresponds exactly to the sys_configs.'
     doc_temps = 'Temperature (K) in MD.'
-    doc_press = 'Pressure (Bar) in MD.'
+    doc_press = 'Pressure (Bar) in MD. Required when ensemble is npt.'
     doc_trj_freq = 'Frequecy of trajectory saved in MD.'
     doc_nsteps = 'Running steps of MD.'
     doc_ensemble = 'Determining which ensemble used in MD, options include “npt” and “nvt”.'
@@ -120,7 +120,7 @@ def model_devi_jobs_args() -> List[Argument]:
     args = [
         Argument("sys_idx", list, optional=False, doc=doc_sys_idx),
         Argument("temps", list, optional=False, doc=doc_temps),
-        Argument("press", list, optional=False, doc=doc_press),
+        Argument("press", list, optional=True, doc=doc_press),
         Argument("trj_freq", int, optional=False, doc=doc_trj_freq),
         Argument("nsteps", int, optional=False, doc=doc_nsteps),
         Argument("ensemble", str, optional=False, doc=doc_ensemble),
@@ -285,9 +285,9 @@ def fp_style_gaussian_args() -> List[Argument]:
         Argument("multiplicity", [int, str],
                  optional=True, default="auto", doc=doc_multiplicity),
         Argument("nproc", int, optional=False, doc=doc_nproc),
-        Argument("charge", int, optional=True, default=0, doc=doc_nproc),
+        Argument("charge", int, optional=True, default=0, doc=doc_charge),
         Argument("fragment_guesses", bool, optional=True, default=False, doc=doc_fragment_guesses),
-        Argument("basis_set", str, optional=True, doc=doc_fragment_guesses),
+        Argument("basis_set", str, optional=True, doc=doc_basis_set),
         Argument("keywords_high_multiplicity", str, optional=True, doc=doc_keywords_high_multiplicity),
     ]
 
@@ -321,12 +321,14 @@ def fp_style_siesta_args() -> List[Argument]:
     doc_kspacing = 'Sample factor in Brillouin zones.'
     doc_mixingweight = 'Proportion a of output Density Matrix to be used for the input Density Matrix of next SCF cycle (linear mixing).'
     doc_NumberPulay = 'Controls the Pulay convergence accelerator.'
+    doc_fp_pp_path = 'Directory of psuedo-potential or numerical orbital files to be used for 02.fp exists.'
+    doc_fp_pp_files = 'Psuedo-potential file to be used for 02.fp. Note that the order of elements should correspond to the order in type_map.'
 
     args = [
         Argument("ecut", int, optional=False, doc=doc_ecut),
         Argument("ediff", float, optional=False, doc=doc_ediff),
         Argument("kspacing", float, optional=False, doc=doc_kspacing),
-        Argument("mixingweight", float, optional=False, doc=doc_mixingweight),
+        Argument("mixingWeight", float, optional=False, doc=doc_mixingweight),
         Argument("NumberPulay", int, optional=False, doc=doc_NumberPulay),
     ]
 
@@ -335,11 +337,13 @@ def fp_style_siesta_args() -> List[Argument]:
     doc_fp_params_siesta = 'Parameters for siesta calculation.'
 
     return [
-        Argument("use_clusters", bool, optional=False, doc=doc_use_clusters),
+        Argument("use_clusters", bool, optional=True, doc=doc_use_clusters),
         Argument("cluster_cutoff", float,
-                 optional=False, doc=doc_cluster_cutoff),
+                 optional=True, doc=doc_cluster_cutoff),
         Argument("fp_params", dict, args, [],
                  optional=False, doc=doc_fp_params_siesta),
+        Argument("fp_pp_path", str, optional=False, doc=doc_fp_pp_path),
+        Argument("fp_pp_files", list, optional=False, doc=doc_fp_pp_files),
     ]
 
 # cp2k
@@ -352,7 +356,7 @@ def fp_style_cp2k_args() -> List[Argument]:
 
     return [
         Argument("user_fp_params", dict, optional=True,
-                 doc=doc_user_fp_params),
+                 doc=doc_user_fp_params, alias=["fp_params"]),
         Argument("external_input_path", str, optional=True,
                  doc=doc_external_input_path),
         Argument("ratio_failed", float, optional=True,

diff --git a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json
@@ -120,8 +120,6 @@
     "shuffle_poscar": false, 
     "fp_task_max": 20, 
     "fp_task_min": 5, 
-    "fp_pp_path": ".", 
-    "fp_pp_files": [], 
     "fp_params": {
 	"cutoff": "400",
 	"rel_cutoff": "50",

diff --git a/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json
@@ -30,7 +30,6 @@
     ], 
     "_comment": " that's all ", 
     "numb_models": 4, 
-    "train_param": "input.json", 
     "default_training_param": {
         "_comment": "that's all", 
         "use_smooth": true, 
@@ -126,7 +125,7 @@
 	"fp_params":	{
 	"ecut":		300,
 	"ediff":	1e-4,
-	"kspacing":	1,
+	"kspacing":	1.0,
 	"mixingWeight": 0.05, 
 	"NumberPulay": 5, 
 	"_comment":	" that's all "

diff --git a/examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json b/examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json
@@ -26,7 +26,6 @@
     ], 
     "_comment": " that's all ", 
     "numb_models": 4, 
-    "train_param": "input.json", 
     "default_training_param": {
         "model": {
         "descriptor": {
@@ -131,7 +130,5 @@
     "shuffle_poscar": false, 
     "fp_task_max": 20, 
     "fp_task_min": 5, 
-    "fp_pp_path": ".", 
-    "fp_pp_files": [], 
     "external_input_path": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/cp2k_dpgen/template.inp"
 }
diff --git a/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json
@@ -3,7 +3,6 @@
     "mass_map":		[12.011, 1.008],
     "init_data_prefix":	"/home/jzzeng/0719dodecane/gen/",
     "init_data_sys":	["init_data"],
-	  "init_multi_systems": true,
     "sys_configs":	[
 	    ["/home/jzzeng/0719dodecane/gen/data.dodecane.atomic"]
     ],
@@ -77,8 +76,6 @@
     "shuffle_poscar":	false,
     "fp_task_max":	1000,
     "fp_task_min":	10,
-    "fp_pp_path":	"/home/jzzeng/",
-    "fp_pp_files":	[],
     "fp_params":	{
       "keywords": "force mn15/6-31g**",
       "nproc":  4,

diff --git a/tests/test_check_examples.py b/tests/test_check_examples.py
@@ -41,20 +41,20 @@
     (run_jdata, p_examples / "run" / "dp1.x-lammps-vasp-et" / "param_elet.json"),
     (run_jdata, p_examples / "run" / "dp2.x-lammps-ABACUS-lcao" / "fcc-al" / "run_param.json"),
     (run_jdata, p_examples / "run" / "dp2.x-lammps-ABACUS-pw" / "fcc-al" / "run_param.json"),
-    #(run_jdata, p_examples / "run" / "dp1.x-lammps-cp2k" / "methane" / "param-ch4.json"),
-    #(run_jdata, p_examples / "run" / "dp1.x-lammps-ABACUS-pw" / "methane" / "param.json"),
-    #(run_jdata, p_examples / "run" / "dp1.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json"),
-    #(run_jdata, p_examples / "run" / "dp1.x_lammps_gaussian" / "dodecane" / "dodecane.json"),
+    (run_jdata, p_examples / "run" / "dp1.x-lammps-cp2k" / "methane" / "param-ch4.json"),
+    (run_jdata, p_examples / "run" / "dp1.x-lammps-ABACUS-pw" / "methane" / "param.json"),
+    (run_jdata, p_examples / "run" / "dp1.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json"),
+    (run_jdata, p_examples / "run" / "dp1.x_lammps_gaussian" / "dodecane" / "dodecane.json"),
     #(run_jdata, p_examples / "run" / "dp-lammps-enhance_sampling" / "param.json"),
     #(run_jdata, p_examples / "run" / "deprecated" / "param-mg-vasp.json"),
     #(run_jdata, p_examples / "run" / "deprecated" / "param-mg-vasp-ucloud.json"),
     #(run_jdata, p_examples / "run" / "deprecated" / "param-pyridine-pwscf.json"),
     #(run_jdata, p_examples / "run" / "deprecated" / "param-h2oscan-vasp.json"),
-    #(run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-cp2k" / "CH4" / "param_CH4.json"),
+    (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-cp2k" / "CH4" / "param_CH4.json"),
     #(run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-pwmat" / "param_CH4.json"),
-    #(run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-siesta" / "dp-lammps-siesta" / "CH4" / "param_CH4.json"),
-    #(run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-vasp" / "Al" / "param_al_all_gpu.json"),
-    #(run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-vasp" / "CH4" / "param_CH4.json"),
+    (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-siesta" / "dp-lammps-siesta" / "CH4" / "param_CH4.json"),
+    (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-vasp" / "Al" / "param_al_all_gpu.json"),
+    (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-vasp" / "CH4" / "param_CH4.json"),
     # machines
     #(run_mdata, p_examples / "machine" / "DeePMD-kit-2.x" / "lebesgue_v2_machine.json"),
     #(run_mdata, p_examples / "machine" / "DeePMD-kit-1.x" / "machine-ali.json"),