fix bug for sys_idx dependent trust level and add option for model_devi_job

README.md

@@ -514,10 +514,10 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
 | *#Exploration*
 | **model_devi_dt** | Float | 0.002 (recommend) | Timestep for MD |
 | **model_devi_skip** | Integer | 0 | Number of structures skipped for fp in each MD
-| **model_devi_f_trust_lo** | Float or List of float | 0.05 | Lower bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
-| **model_devi_f_trust_hi** | Float or List of float | 0.15 | Upper bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
-| **model_devi_v_trust_lo**  | Float or List of float | 1e10 | Lower bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
-| **model_devi_v_trust_hi**  | Float or List of float | 1e10 | Upper bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
+| **model_devi_f_trust_lo** | Float or List of float or Dict[str, float] | 0.05 | Lower bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
+| **model_devi_f_trust_hi** | Float or List of float or Dict[str, float] | 0.15 | Upper bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
+| **model_devi_v_trust_lo**  | Float or List of float or Dict[str, float] | 1e10 | Lower bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
+| **model_devi_v_trust_hi**  | Float or List of float or Dict[str, float] | 1e10 | Upper bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
 | model_devi_adapt_trust_lo  | Boolean | False | Adaptively determines the lower trust levels of force and virial. This option should be used together with `model_devi_numb_candi_f`,  `model_devi_numb_candi_v` and optionally with `model_devi_perc_candi_f` and `model_devi_perc_candi_v`. `dpgen` will make two sets: 1. From the frames with force model deviation lower than `model_devi_f_trust_hi`, select `max(model_devi_numb_candi_f, model_devi_perc_candi_f*n_frames)` frames with largest force model deviation. 2. From the frames with virial model deviation lower than `model_devi_v_trust_hi`, select `max(model_devi_numb_candi_v, model_devi_perc_candi_v*n_frames)` frames with largest virial model deviation. The union of the two sets is made as candidate dataset|
 | model_devi_numb_candi_f  | Int | 10 | See `model_devi_adapt_trust_lo`.|
 | model_devi_numb_candi_v  | Int | 0  | See `model_devi_adapt_trust_lo`.|
@@ -536,7 +536,8 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
 | **model_devi_jobs["ensembles"]** | String             | "nvt"                                    | Determining which ensemble used in MD, **options** include “npt” and “nvt”. |
 | model_devi_jobs["neidelay"] | Integer             | "10"                                    | delay building until this many steps since last build |
 | model_devi_jobs["taut"] | Float          | "0.1"                                    | Coupling time of thermostat (ps) |
-| model_devi_jobs["taup"] | Float             | "0.5"                                    | Coupling time of barostat (ps)
+| model_devi_jobs["taup"] | Float             | "0.5"                                    | Coupling time of barostat (ps) |
+| model_devi_jobs["model_devi_f_trust_lo"] <br> model_devi_jobs["model_devi_f_trust_hi"] <br> model_devi_jobs["model_devi_v_trust_lo"] <br> model_devi_jobs["model_devi_v_trust_hi"] | Float or Dict[str, float] | See global model_devi config above like **model_devi_f_trust_lo**. For dict, should be set for each index in sys_idx, respectively. |
 | *#Labeling*
 | **fp_style** | string                | "vasp"                                                       | Software for First Principles. **Options** include “vasp”, “pwscf”, “siesta” and “gaussian” up to now. |
 | **fp_task_max** | Integer            | 20                                                           | Maximum of  structures to be calculated in `02.fp` of each iteration. |

dpgen/generator/arginfo.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import Dict, List
 from dargs import Argument, Variant
 
 from dpgen.arginfo import general_mdata_arginfo
@@ -90,6 +90,10 @@ def model_devi_jobs_args() -> List[Argument]:
     doc_neidelay = 'delay building until this many steps since last build.'
     doc_taut = 'Coupling time of thermostat (ps).'
     doc_taup = 'Coupling time of barostat (ps).'
+    doc_model_devi_f_trust_lo = 'Lower bound of forces for the selection. If dict, should be set for each index in sys_idx, respectively.'
+    doc_model_devi_f_trust_hi = 'Upper bound of forces for the selection. If dict, should be set for each index in sys_idx, respectively.'
+    doc_model_devi_v_trust_lo = 'Lower bound of virial for the selection. If dict, should be set for each index in sys_idx, respectively. Should be used with DeePMD-kit v2.x.'
+    doc_model_devi_v_trust_hi = 'Upper bound of virial for the selection. If dict, should be set for each index in sys_idx, respectively. Should be used with DeePMD-kit v2.x.'
 
     args = [
         Argument("sys_idx", list, optional=False, doc=doc_sys_idx),
@@ -101,6 +105,14 @@ def model_devi_jobs_args() -> List[Argument]:
         Argument("neidelay", int, optional=True, doc=doc_neidelay),
         Argument("taut", float, optional=True, doc=doc_taut),
         Argument("taup", float, optional=True, doc=doc_taup),
+        Argument("model_devi_f_trust_lo", [
+                 float, dict], optional=False, doc=doc_model_devi_f_trust_lo),
+        Argument("model_devi_f_trust_hi", [
+                 float, dict], optional=False, doc=doc_model_devi_f_trust_hi),
+        Argument("model_devi_v_trust_lo", [
+                 float, dict], optional=False, doc=doc_model_devi_v_trust_lo),
+        Argument("model_devi_v_trust_hi", [
+                 float, dict], optional=False, doc=doc_model_devi_v_trust_hi),
     ]
 
     doc_model_devi_jobs = 'Settings for exploration in 01.model_devi. Each dict in the list corresponds to one iteration. The index of model_devi_jobs exactly accord with index of iterations'
@@ -110,10 +122,10 @@ def model_devi_jobs_args() -> List[Argument]:
 def model_devi_lmp_args() -> List[Argument]:
     doc_model_devi_dt = 'Timestep for MD. 0.002 is recommend.'
     doc_model_devi_skip = 'Number of structures skipped for fp in each MD.'
-    doc_model_devi_f_trust_lo = 'Lower bound of forces for the selection. If list, should be set for each index in sys_configs, respectively.'
-    doc_model_devi_f_trust_hi = 'Upper bound of forces for the selection. If list, should be set for each index in sys_configs, respectively.'
-    doc_model_devi_v_trust_lo = 'Lower bound of virial for the selection. If list, should be set for each index in sys_configs, respectively. Should be used with DeePMD-kit v2.x.'
-    doc_model_devi_v_trust_hi = 'Upper bound of virial for the selection. If list, should be set for each index in sys_configs, respectively. Should be used with DeePMD-kit v2.x.'
+    doc_model_devi_f_trust_lo = 'Lower bound of forces for the selection. If list or dict, should be set for each index in sys_configs, respectively.'
+    doc_model_devi_f_trust_hi = 'Upper bound of forces for the selection. If list or dict, should be set for each index in sys_configs, respectively.'
+    doc_model_devi_v_trust_lo = 'Lower bound of virial for the selection. If list or dict, should be set for each index in sys_configs, respectively. Should be used with DeePMD-kit v2.x.'
+    doc_model_devi_v_trust_hi = 'Upper bound of virial for the selection. If list or dict, should be set for each index in sys_configs, respectively. Should be used with DeePMD-kit v2.x.'
     doc_model_devi_adapt_trust_lo = 'Adaptively determines the lower trust levels of force and virial. This option should be used together with model_devi_numb_candi_f, model_devi_numb_candi_v and optionally with model_devi_perc_candi_f and model_devi_perc_candi_v. dpgen will make two sets:\n\n\
 - 1. From the frames with force model deviation lower than model_devi_f_trust_hi, select max(model_devi_numb_candi_f, model_devi_perc_candi_f*n_frames) frames with largest force model deviation. \n\n\
 - 2. From the frames with virial model deviation lower than model_devi_v_trust_hi, select max(model_devi_numb_candi_v, model_devi_perc_candi_v*n_frames) frames with largest virial model deviation. \n\n\
@@ -134,13 +146,13 @@ def model_devi_lmp_args() -> List[Argument]:
         Argument("model_devi_skip", int, optional=False,
                  doc=doc_model_devi_skip),
         Argument("model_devi_f_trust_lo", [
-                 float, list], optional=False, doc=doc_model_devi_f_trust_lo),
+                 float, list, dict], optional=False, doc=doc_model_devi_f_trust_lo),
         Argument("model_devi_f_trust_hi", [
-                 float, list], optional=False, doc=doc_model_devi_f_trust_hi),
+                 float, list, dict], optional=False, doc=doc_model_devi_f_trust_hi),
         Argument("model_devi_v_trust_lo", [
-                 float, list], optional=False, doc=doc_model_devi_v_trust_lo),
+                 float, list, dict], optional=False, doc=doc_model_devi_v_trust_lo),
         Argument("model_devi_v_trust_hi", [
-                 float, list], optional=False, doc=doc_model_devi_v_trust_hi),
+                 float, list, dict], optional=False, doc=doc_model_devi_v_trust_hi),
         Argument("model_devi_adapt_trust_lo", bool, optional=True,
                  doc=doc_model_devi_adapt_trust_lo),
         Argument("model_devi_numb_candi_f", int, optional=True,

dpgen/generator/run.py

@@ -1902,6 +1902,8 @@ def _make_fp_vasp_inner (modd_path,
     def _trust_limitation_check(sys_idx, lim):
         if isinstance(lim, list):
             sys_lim = lim[sys_idx]
+        elif isinstance(lim, dict):
+            sys_lim = lim[str(sys_idx)]
         else:
             sys_lim = lim
         return sys_lim
@@ -1912,10 +1914,10 @@ def _trust_limitation_check(sys_idx, lim):
         modd_system_task.sort()
         if model_devi_engine in ('lammps', 'gromacs', 'calypso'):
             # convert global trust limitations to local ones
-            f_trust_lo_sys = _trust_limitation_check(ss, f_trust_lo)
-            f_trust_hi_sys = _trust_limitation_check(ss, f_trust_hi)
-            v_trust_lo_sys = _trust_limitation_check(ss, v_trust_lo)
-            v_trust_hi_sys = _trust_limitation_check(ss, v_trust_hi)
+            f_trust_lo_sys = _trust_limitation_check(int(ss), f_trust_lo)
+            f_trust_hi_sys = _trust_limitation_check(int(ss), f_trust_hi)
+            v_trust_lo_sys = _trust_limitation_check(int(ss), v_trust_lo)
+            v_trust_hi_sys = _trust_limitation_check(int(ss), v_trust_hi)
 
             # assumed e -> v
             if not model_devi_adapt_trust_lo:
@@ -2453,10 +2455,6 @@ def _make_fp_vasp_configs(iter_index,
                           jdata):
     fp_task_max = jdata['fp_task_max']
     model_devi_skip = jdata['model_devi_skip']
-    v_trust_lo = jdata.get('model_devi_v_trust_lo', 1e10)
-    v_trust_hi = jdata.get('model_devi_v_trust_hi', 1e10)
-    f_trust_lo = jdata['model_devi_f_trust_lo']
-    f_trust_hi = jdata['model_devi_f_trust_hi']
     type_map = jdata['type_map']
     iter_name = make_iter_name(iter_index)
     work_path = os.path.join(iter_name, fp_name)
@@ -2469,6 +2467,20 @@ def _make_fp_vasp_configs(iter_index,
         cur_job = json.load(open(os.path.join(modd_path, 'cur_job.json'), 'r'))
         if 'task_min' in cur_job :
             task_min = cur_job['task_min']
+    else:
+        cur_job = {}
+    # support iteration dependent trust levels
+    v_trust_lo = cur_job.get('model_devi_v_trust_lo', jdata.get('model_devi_v_trust_lo', 1e10))
+    v_trust_hi = cur_job.get('model_devi_v_trust_hi', jdata.get('model_devi_v_trust_hi', 1e10))
+    if cur_job.get('model_devi_f_trust_lo') is not None:
+        f_trust_lo = cur_job.get('model_devi_f_trust_lo')
+    else:
+        f_trust_lo = jdata['model_devi_f_trust_lo']
+    if cur_job.get('model_devi_f_trust_hi') is not None:
+        f_trust_hi = cur_job.get('model_devi_f_trust_hi')
+    else:
+        f_trust_hi = jdata['model_devi_f_trust_hi']
+
     # make configs
     fp_tasks = _make_fp_vasp_inner(modd_path, work_path,
                                    model_devi_skip,

tests/generator/context.py

@@ -27,6 +27,7 @@
 param_abacus_file = 'param-pyridine-abacus.json'
 param_abacus_post_file = 'param-methane-abacus.json'
 param_amber_file = "param-amber.json"
+param_multiple_trust_file = 'param-mg-vasp-multi-trust.json'
 
 def my_file_cmp(test, f0, f1):
     with open(f0) as fp0 :

tests/generator/param-mg-vasp-multi-trust.json

@@ -0,0 +1,111 @@
+{    
+    "type_map":		["Mg", "Al"],
+    "mass_map":		[24, 27],
+
+    "init_data_prefix":	"data",
+    "init_data_sys":	["deepmd"
+			],
+    "init_batch_size":	[16],
+    "sys_configs":	[
+	["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000000/POSCAR"],
+	["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000001/POSCAR"]
+    ],
+    "_comment":		"0  1  2  3",
+    "_comment":		"4  5  6  7",
+    "sys_batch_size":	[1, 1
+			],
+
+    "_comment":		" 00.train ",
+    "numb_models":	4,
+    "train_param":	"input.json",
+    "default_training_param" : {
+	"_comment": " model parameters",
+	"use_smooth":		true,
+	"sel_a":		[90],
+	"rcut_smth":		2.00,
+	"rcut":			6.00,
+	"filter_neuron":	[25, 50, 100],
+	"filter_resnet_dt":	false,
+	"n_axis_neuron":	12,
+	"n_neuron":		[240, 240, 240],
+	"resnet_dt":		true,
+	"coord_norm":		true,
+	"type_fitting_net":	false,
+
+	"_comment": " traing controls",
+	"systems":		[],
+	"set_prefix":		"set",    
+	"stop_batch":		400000,
+	"batch_size":		1,
+	"start_lr":		0.002,
+	"decay_steps":		2000,
+	"decay_rate":		0.95,
+	"seed":			0,
+
+	"start_pref_e":		0.02,
+	"limit_pref_e":		2,
+	"start_pref_f":		1000,
+	"limit_pref_f":		1,
+	"start_pref_v":		0.0,
+	"limit_pref_v":		0.0,
+
+	"_comment": " display and restart",
+	"_comment": " frequencies counted in batch",
+	"disp_file":		"lcurve.out",
+	"disp_freq":		2000,
+	"numb_test":		10,
+	"save_freq":		20000,
+	"save_ckpt":		"model.ckpt",
+	"load_ckpt":		"model.ckpt",
+	"disp_training":	true,
+	"time_training":	true,
+	"profiling":		false,
+	"profiling_file":	"timeline.json",
+
+	"_comment":		"that's all"
+    },
+
+    "_comment":		" 01.model_devi ",
+    "_comment": "model_devi_skip: the first x of the recorded frames",
+    "model_devi_dt":		0.002,
+    "model_devi_skip":		0,
+    "model_devi_f_trust_lo":	[0.000, 0.050],
+    "model_devi_f_trust_hi":	{"1": 0.100, "0": 0.150},
+    "model_devi_e_trust_lo":	1e10,
+    "model_devi_e_trust_hi":	1e10,
+    "model_devi_clean_traj":	false,
+    "model_devi_jobs":	[
+	{"sys_idx": [0, 1], "temps": [50,100], "press": [1.0,2.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "00"}
+    ],
+
+    "_comment":		" 02.fp ",
+    "fp_style":		"vasp",
+    "shuffle_poscar":	false,
+    "fp_task_max":	100,
+    "fp_task_min":	10,
+    "fp_pp_path":	".",
+    "fp_pp_files":	["vasp/potcars/POTCAR.mg", "vasp/potcars/POTCAR.al"],
+    "_comment":		" user provided vasp script ",
+    "user_fp_params": {
+	"PREC":		"A",
+	"ENCUT":	600,
+	"ISYM":		0,
+	"ALGO":		"fast",
+	"EDIFF":	1e-05,
+	"LREAL":	"A",
+	"NPAR":		1,
+	"KPAR":		1,
+	"NELMIN":	4,
+	"ISIF":		2,
+	"ISMEAR":	1,
+	"SIGMA":	0.25,
+	"IBRION":	-1,
+	"NSW":		0,
+	"LWAVE":	false,
+	"LCHARG":	false,
+	"PSTRESS":	0,
+	"KSPACING":	0.16,
+	"KGAMMA":	false
+    },
+    "_comment":		" that's all "
+}

tests/generator/test_make_fp.py

@@ -23,6 +23,7 @@
 from .context import ref_cp2k_file_exinput
 from .context import machine_file
 from .context import param_diy_file
+from .context import param_multiple_trust_file
 from .context import make_kspacing_kpoints
 from .context import my_file_cmp
 from .context import setUpModule
@@ -345,6 +346,16 @@ def _check_potcar(testCase, idx, fp_pp_path, fp_pp_files) :
 
 
 def _check_sel(testCase, idx, fp_task_max, flo, fhi):
+
+    def _trust_limitation_check(sys_idx, lim):
+        if isinstance(lim, list):
+            sys_lim = lim[sys_idx]
+        elif isinstance(lim, dict):
+            sys_lim = lim[str(sys_idx)]
+        else:
+            sys_lim = lim
+        return sys_lim
+
     fp_path = os.path.join('iter.%06d' % idx, '02.fp')
     candi_files = glob.glob(os.path.join(fp_path, 'candidate.shuffled.*.out'))
     candi_files.sort()
@@ -358,6 +369,8 @@ def _check_sel(testCase, idx, fp_task_max, flo, fhi):
                 f_idx.append(ii.split()[1])
         md_task = md_task[:fp_task_max]
         f_idx = f_idx[:fp_task_max]
+        flo = _trust_limitation_check(int(sidx), flo)
+        fhi = _trust_limitation_check(int(sidx), fhi)
         for tt,ff in zip(md_task, f_idx):
             md_value = np.loadtxt(os.path.join(tt, 'model_devi.out'))
             fvalue = md_value[int(ff)][4]
@@ -795,6 +808,41 @@ def test_make_fp_vasp_ele_temp(self):
         # checked elsewhere
         # _check_potcar(self, 0, jdata['fp_pp_path'], jdata['fp_pp_files'])
         shutil.rmtree('iter.000000')
+
+    def test_make_fp_vasp_multiple_trust_level(self):
+        # Verify if sys_idx dependent trust level could be read.
+        setUpModule()
+        if os.path.isdir('iter.000000') :
+            shutil.rmtree('iter.000000')
+        with open (param_multiple_trust_file, 'r') as fp :
+            jdata = json.load (fp)
+        fp.close()
+        with open (machine_file, 'r') as fp:
+            mdata = json.load (fp)
+        fp.close()
+        md_descript = []
+        ele_temp = []
+        nsys = 2
+        nmd = 3
+        n_frame = 10
+        for ii in range(nsys) :
+            tmp = []
+            for jj in range(nmd) :
+                tmp.append(np.arange(0, 0.29, 0.29/10))
+            md_descript.append(tmp)
+            ele_temp.append([np.random.random() * 100000] * nmd)
+        atom_types = [0, 1, 0, 1]
+        type_map = jdata['type_map']
+        _make_fake_md(0, md_descript, atom_types, type_map, ele_temp = ele_temp)
+        make_fp(0, jdata, {})
+        _check_sel(self, 0, jdata['fp_task_max'], jdata['model_devi_f_trust_lo'], jdata['model_devi_f_trust_hi'])
+        _check_poscars(self, 0, jdata['fp_task_max'], jdata['type_map'])
+        _check_incar_ele_temp(self, 0, ele_temp)
+        _check_kpoints_exists(self, 0)
+        _check_kpoints(self,0)
+        # checked elsewhere
+        # _check_potcar(self, 0, jdata['fp_pp_path'], jdata['fp_pp_files'])
+        shutil.rmtree('iter.000000')
 
 
 class TestMakeFPGaussian(unittest.TestCase):