update customized CV

deepmodeling · Aug 28, 2023 · d6f2d70 · d6f2d70
1 parent 3417c11
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diff --git a/README.md b/README.md
@@ -66,6 +66,13 @@ rid submit -i ./tests/data/000 -c ./rid/template/rid_gmx_dih.json -m ./rid/templ
 ```
 After successful submission you can login into your Bohrium account at [deepmodeling k8s](https://workflows.deepmodeling.com/) to monitor your job status, where the workflow is displayed using the `Argo` UI.
 
+If you want to run Rid-kit using your own customized CVs, an example is given (see [configure simulations](docs/source/rid_configuration.md) for more details):
+
+**Note** that the length of **angular_mask**, **weights** and **kappas** keys in rid.json should all be equal to the length of your defined CV number.
+```bash
+rid submit -i ./tests/data/001 -c ./rid/template/rid_gmx_custom.json -m ./rid/template/machine_bohrium_k8s.json
+```
+
 You can also run the example on a Slurm machine (But you need to configure a conda environment on the slurm, see [Installation](docs/source/install.md))
 
 ```bash

diff --git a/rid/op/run_exploration.py b/rid/op/run_exploration.py
@@ -173,7 +173,7 @@ def execute(
 
             if op_in["cv_file"] is not None:
                 for file in op_in["cv_file"]:
-                    if file.name != "colvar":
+                    if os.path.basename(file).endswith("pdb"):
                         if not os.path.islink(file.name):
                             os.symlink(file, file.name)
 

diff --git a/rid/template/machine_bohrium_k8s_mcmc.json b/rid/template/machine_bohrium_k8s_mcmc.json
@@ -24,7 +24,6 @@
                     "input_data":{
                         "api_version":2,
                         "job_type": "container",
-                        "job_group_id": "",
                         "log_file": "tmp_log",
                         "job_name": "train",
                         "scass_type":"c8_m32_1 * NVIDIA V100",
@@ -55,7 +54,6 @@
                     "input_data":{
                         "api_version":2,
                         "job_type": "container",
-                        "job_group_id": "",
                         "log_file": "tmp_log",
                         "job_name": "train",
                         "scass_type":"c8_m32_1 * NVIDIA V100",

diff --git a/rid/template/rid_gmx_custom.json b/rid/template/rid_gmx_custom.json
@@ -0,0 +1,86 @@
+{
+    "name": "test",
+    "numb_walkers": 4,
+    "numb_iters": 5,
+    "trust_lvl_1": 2,
+    "trust_lvl_2": 3,
+    "init_models": [],
+
+    "CV": {
+        "mode": "custom",
+        "angular_mask": [ 1, 1 ],
+        "weights": [ 1, 1 ],
+        "cv_file":["plumed.dat"]
+    },
+
+    "ExploreMDConfig": {
+        "nsteps": 50000,
+        "type": "gmx",
+        "temperature": 300,
+        "output_freq": 50,
+        "ref-t": "300 300",
+        "verlet-buffer-tolerance":"-1",
+        "rlist": 1,
+        "rvdw": 0.9,
+        "rvdw-switch": 0,
+        "rcoulomb": 0.9,
+        "rcoulomb-switch": 0,
+        "epsilon-r":1,
+        "epsilon-rf":80,
+        "dt": 0.002,
+        "fourierspacing": "0.12",
+        "output_mode": "single",
+        "ntmpi": 1,
+        "nt": 8,
+        "max_warning": 2
+    },
+
+    "SelectorConfig": {
+        "numb_cluster_lower": 12,
+        "numb_cluster_upper": 22,
+        "cluster_threshold": 1.5,
+        "max_selection": 30,
+        "numb_cluster_threshold": 6,
+        "slice_mode": "gmx"
+    },
+
+    "LabelMDConfig": {
+        "nsteps": 50000,
+        "temperature":300,
+        "method": "restrained",
+        "type": "gmx",
+        "output_freq": 50,
+        "ref-t": "300 300",
+        "rlist": 1,
+        "verlet-buffer-tolerance":"-1",
+        "rvdw": 0.9,
+        "rvdw-switch": 0,
+        "rcoulomb": 0.9,
+        "rcoulomb-switch": 0,
+        "epsilon-r":1,
+        "epsilon-rf":80,
+        "dt": 0.002,
+        "fourierspacing": "0.12",
+        "output_mode": "single",
+        "ntmpi": 1,
+        "nt": 8,
+        "max_warning": 2,
+        "kappas": [ 500, 500 ],
+        "std_threshold": 1.5
+    },
+
+    "Train": {
+        "numb_models": 4,
+        "neurons": [40, 40, 40, 40],
+        "resnet": true,
+        "batch_size": 128,
+        "epoches": 8000,
+        "init_lr": 0.0008,
+        "decay_steps": 120,
+        "decay_rate": 0.96,
+        "drop_out_rate": 0.1,
+        "numb_threads": 8,
+        "use_mix": false,
+        "restart": false
+    }
+}