Example_dp2.x_lmp_gaussian

doc/troubleshooting/common-errors.md

@@ -28,4 +28,4 @@ Some common reasons are as follows:
 2. You may have something wrong in your input files, which causes the process to fail.
 
 ## RuntimeError: find too many unsuccessfully terminated jobs.
-The ratio of failed jobs is larger than ratio_failure. You can set a high value for ratio_failure or check if there is something wrong with your input files. 
+The ratio of failed jobs is larger than ratio_failure. You can set a high value for ratio_failure or check if there is something wrong with your input files. 

dpgen/generator/arginfo.py

@@ -278,6 +278,7 @@ def fp_style_gaussian_args() -> List[Argument]:
     doc_basis_set = 'Custom basis set.'
     doc_keywords_high_multiplicity = ('Keywords for points with multiple raicals. `multiplicity` should be `auto`. '
                                       'If not set, fallback to normal keywords.')
+
 
     args = [
         Argument("keywords", [str, list],
@@ -302,6 +303,7 @@ def fp_style_gaussian_args() -> List[Argument]:
                           'hydrogen atom. When the outer atom is a hydrogen atom, the outer atom will be '
                           'kept. In this case, other atoms out of the soft cutoff radius will be removed.')
     doc_fp_params_gaussian = 'Parameters for Gaussian calculation.'
+    doc_ratio_failed = 'Check the ratio of unsuccessfully terminated jobs. If too many FP tasks are not converged, RuntimeError will be raised.'
 
     return [
         Argument("use_clusters", bool, optional=True, default=False, doc=doc_use_clusters),
@@ -311,6 +313,8 @@ def fp_style_gaussian_args() -> List[Argument]:
         Argument("cluster_minify", bool, optional=True, default=False, doc=doc_cluster_minify),
         Argument("fp_params", dict, args, [],
                  optional=False, doc=doc_fp_params_gaussian),
+        Argument("ratio_failed", float, optional=True,
+                 doc=doc_ratio_failed),
     ]
 
 

examples/run/dp2.x-lammps-gaussian/machine.json

@@ -0,0 +1,110 @@
+{
+  "api_version": "1.0",
+  "deepmd_version": "2.1.0",
+  "train" :
+  {
+      "command": "dp",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "huyongxin1015@163.com",
+          "password": "0415fnmsM.",
+          "program_id": 10330,
+            "keep_backup":true,
+            "input_data":{
+                "job_type": "indicate",
+                "log_file": "00*/train.log",
+                "grouped":true,
+                "job_name": "dpgen_train_job",
+                "disk_size": 100,
+                "scass_type":"c4_m15_1 * NVIDIA T4",
+                "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"],
+                "checkpoint_time":30,
+                "platform": "ali",
+                "image_name":"LBG_DeePMD-kit_2.1.0_v1",
+                "on_demand":0
+            }
+        }
+      },
+      "resources": {
+	"batch_type": "Lebesgue",
+        "number_node": 1,
+        "cpu_per_node": 4,
+        "gpu_per_node": 1,
+        "queue_name": "T4_4_15",
+        "group_size": 1
+      }
+    },
+  "model_devi":
+    {
+      "command": "lmp",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "huyongxin1015@163.com",
+          "password": "0415fnmsM.",
+          "program_id": 10330,
+            "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":"c4_m15_1 * NVIDIA T4",
+              "platform": "ali",
+              "image_name":"LBG_DeePMD-kit_2.1.0_v1",
+              "on_demand":0
+            }
+        }
+      },
+      "resources": {
+	"batch_type": "Lebesgue",
+        "number_node": 1,
+        "cpu_per_node": 4,
+        "gpu_per_node": 1,
+        "queue_name": "T4_4_15",
+        "group_size": 50
+      }
+    },
+  "fp":
+    {
+      "command": "g09 < input > output ||:",
+      "machine": {
+        "batch_type": "Lebesgue",
+        "context_type": "LebesgueContext",
+        "local_root" : "./",
+        "remote_profile":{
+          "email": "huyongxin1015@163.com",
+          "password": "0415fnmsM.",
+          "program_id": 10330,
+            "input_data":{
+              "api_version":2,
+              "job_type": "indicate",
+              "log_file": "task*/fp.log",
+              "grouped":true,
+              "job_name": "dpgen_fp_job",
+              "disk_size": 100,
+              "scass_type":"c16_m32_cpu",
+              "platform": "ali",
+              "image_name":"LBG_Gaussian_09_v2",
+              "on_demand":0
+            }
+        }
+      },
+      "resources": {
+	"batch_type": "Lebesgue",
+        "source_list": ["/root/g09.sh"],
+        "number_node": 1,
+        "cpu_per_node": 16,
+        "gpu_per_node": 0,
+        "queue_name": "CPU",
+        "group_size": 10
+      }
+    }
+}
+

examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json

@@ -0,0 +1,140 @@
+{
+    "type_map": [
+        "H", 
+        "C",
+        "N"
+    ], 
+    "mass_map": [
+        1, 
+        12,
+        14
+    ], 
+    "init_data_prefix": "./data/deepmd/", 
+    "init_data_sys": [
+        "data.000","data.001","data.002","data.003","data.004","data.005"
+    ],
+    "init_batch_size":  ["auto","auto","auto","auto","auto","auto"],
+    "sys_configs": [
+        [
+            "./data/md_sys/data.ch4n2"
+        ]
+    ], 
+    "_comment": " that's all ", 
+    "numb_models": 4,
+    "sys_format":"lammps/lmp",  
+    "default_training_param": {
+        "model": {
+            "type_map": [
+                "H",
+                "C",
+                "N"
+            ],
+            "descriptor": {
+                "type": "se_e2_a",
+                "sel": [
+                    16,
+                    4,
+                    4
+                ],
+                "rcut_smth": 0.5,
+                "rcut": 5.0,
+                "neuron": [
+                    25,
+                    50,
+                    100
+                ],
+                "resnet_dt": true,
+                "axis_neuron": 12,
+                "seed": 1
+            },
+            "fitting_net": {
+                "neuron": [
+                    120,
+                    120,
+                    120
+                ],
+                "resnet_dt": false,
+                "seed": 1
+            }
+        },
+        "learning_rate": {
+            "type": "exp",
+            "start_lr": 0.001,
+            "decay_steps": 200
+        },
+        "loss": {
+            "start_pref_f": 1000,
+            "limit_pref_f": 1,
+            "start_pref_v": 0.0,
+            "limit_pref_v": 0.0
+        },
+        "training": {
+            "_set_prefix": "set",
+            "stop_batch": 20000,
+            "_batch_size": 1,
+            "disp_file": "lcurve.out",
+            "disp_freq": 1000,
+            "numb_test": 4,
+            "save_freq": 1000,
+            "save_ckpt": "model.ckpt",
+            "disp_training": true,
+            "time_training": true,
+            "profiling": false,
+            "profiling_file": "timeline.json",
+            "_comment": "that's all"
+        }
+    },
+    "model_devi_dt": 0.002, 
+    "model_devi_skip": 0, 
+    "model_devi_f_trust_lo": 0.02, 
+    "model_devi_f_trust_hi": 1.95, 
+    "model_devi_clean_traj": true, 
+    "model_devi_jobs": [
+        {
+            "sys_idx": [
+                0
+            ], 
+            "temps": [
+                100
+            ], 
+            "press": [
+                1
+            ], 
+            "trj_freq": 10, 
+            "nsteps": 2000, 
+            "ensemble": "nvt", 
+            "_idx": "00"
+        }, 
+        {
+            "sys_idx": [
+                0
+            ], 
+            "temps": [
+                100
+            ], 
+            "press": [
+                1
+            ], 
+            "trj_freq": 10, 
+            "nsteps": 5000, 
+            "ensemble": "nvt", 
+            "_idx": "01"
+        }
+
+    ], 
+    "use_clusters": true,
+    "cluster_cutoff": 5.0,
+    "cluster_minify": true,
+    "use_relative": true,
+    "epsilon": 1.0,
+    "ratio_failed": 0.20, 
+    "fp_style": "gaussian",
+    "shuffle_poscar": false,
+    "fp_task_max": 20,
+    "fp_task_min": 5,
+    "fp_params":{
+            "keywords": "force B3LYP 6-31g(d,p) nosymm",
+            "nproc":2 ,
+            "multiplicity": "auto"
+    }
+}

tests/test_check_examples.py

@@ -55,6 +55,7 @@
     (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" / "dp2.x-lammps-gaussian" / "param_C4H16N4_deepmd-kit-2.0.1.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"),
@@ -72,6 +73,7 @@
     (run_mdata, p_examples / "CH4-refact-dpdispatcher" / "machine-dpcloudserver.json"),
     (run_mdata, p_examples / "run" / "dp2.x-lammps-ABACUS-lcao" / "fcc-al" / "machine.json"),
     (run_mdata, p_examples / "run" / "dp2.x-lammps-ABACUS-pw" / "fcc-al" / "machine.json"),
+    (run_mdata, p_examples / "run" / "dp2.x-lammps-gaussian" / "machine.json"),
     #(run_mdata, p_examples / "run" / "dp2.x-gromacs-gaussian" / "machine.json"),
     (simplify_mdata, p_examples / "simplify-MAPbI3-scan-lebesgue" / "simplify_example" / "machine.json"),
 )