Merge pull request #110 from Exabyte-io/feat/SOF-7194

SOF-7194: preliminary deepmd support on the web platform

applications/application_data.yml

@@ -1,3 +1,4 @@
+deepmd: !include 'applications/deepmd.yml'
 espresso: !include 'applications/espresso.yml'
 exabyteml: !include 'applications/exabyteml.yml'
 jupyterLab: !include 'applications/jupyterLab.yml'

applications/deepmd.yml

@@ -0,0 +1,7 @@
+name: deepmd
+shortName: deepmd
+summary: DeePMD
+defaultVersion: '2.0.2'
+versions:
+  - version: '2.0.2'
+    isDefault: true

assets/deepmd/dp_train_se_e2_r.j2.json

@@ -0,0 +1,67 @@
+{
+    "model": {
+        "type_map": [
+            "O",
+            "H"
+        ],
+        "descriptor": {
+            "type": "se_e2_r",
+            "sel": [
+                23,
+                46
+            ],
+            "rcut_smth": 0.50,
+            "rcut": 5.00,
+            "neuron": [
+                5,
+                5,
+                5
+            ],
+            "resnet_dt": false,
+            "seed": 1
+        },
+        "fitting_net": {
+            "neuron": [
+                60,
+                60,
+                60
+            ],
+            "resnet_dt": true,
+            "seed": 1
+        }
+    },
+    "learning_rate": {
+        "type": "exp",
+        "decay_steps": 1000,
+        "start_lr": 0.005,
+        "stop_lr": 3.51e-6
+    },
+    "loss": {
+        "start_pref_e": 0.02,
+        "limit_pref_e": 1,
+        "start_pref_f": 1000,
+        "limit_pref_f": 1,
+        "start_pref_v": 0,
+        "limit_pref_v": 0
+    },
+    "training": {
+        "training_data": {
+            "systems": [
+                "./training/"
+            ],
+            "batch_size": "auto"
+        },
+        "validation_data": {
+            "systems": [
+                "./validation/"
+            ],
+            "batch_size": "auto"
+        },
+        "numb_steps": 301,
+        "seed": 1,
+        "disp_file": "lcurve.out",
+        "disp_freq": 10,
+        "numb_test": 1,
+        "save_freq": 100
+    }
+}

assets/deepmd/espresso_cp_to_deepmd.j2.py

@@ -0,0 +1,23 @@
+import dpdata
+import numpy as np
+
+# https://docs.deepmodeling.com/projects/dpdata/en/master/formats/QECPTrajFormat.html
+data = dpdata.LabeledSystem("cp", fmt="qe/cp/traj")
+print("Dataset contains total {0} frames".format(len(data)))
+
+# randomly choose 20% index for validation_data
+size = len(data)
+size_validation = round(size * 0.2)
+
+index_validation = np.random.choice(size, size=size_validation, replace=False)
+index_training = list(set(range(size)) - set(index_validation))
+
+data_training = data.sub_system(index_training)
+data_validation = data.sub_system(index_validation)
+
+print("Using {0} frames as training set".format(len(data_training)))
+print("Using {0} frames as validation set".format(len(data_validation)))
+
+# save training and validation sets
+data_training.to_deepmd_npy("./training")
+data_validation.to_deepmd_npy("./validation")

assets/deepmd/espresso_to_lammps_structure.j2.py

@@ -0,0 +1,10 @@
+import dpdata
+
+# load cp data files
+# https://docs.deepmodeling.com/projects/dpdata/en/master/formats/QECPTrajFormat.html
+system = dpdata.LabeledSystem("cp", fmt="qe/cp/traj")
+
+# convert dpdata to lammps format
+# below procedure will convert input QE structure to lammps format, user may
+# want to generate supercell or other complex structure for lammps calculation
+system.to_lmp("system.lmp")

assets/deepmd/in.lammps

@@ -0,0 +1,25 @@
+# LAMMPS input, deepmd-kit version. Built from bulk water calculation.
+
+units           metal
+boundary        p p p
+atom_style      atomic
+
+neighbor        2.0 bin
+neigh_modify    every 10 delay 0 check no
+
+read_data       system.lmp
+mass            1 16
+mass            2 2
+
+pair_style	    deepmd ./graph.pb
+pair_coeff      * *
+
+velocity        all create 330.0 23456789
+
+fix             1 all nvt temp 330.0 330.0 0.5
+timestep        0.0005
+thermo_style    custom step pe ke etotal temp press vol
+thermo          100
+dump            1 all custom 100 system.dump id type x y z
+
+run             100

assets/espresso/cp.j2.in

@@ -27,6 +27,9 @@
     electron_dynamics = 'verlet'
     electron_velocities = 'zero'
     emass = {{ dynamics.electronMass }}
+!! consider the below parameters if orthogonalization fails
+!   orthogonalization = 'ortho'
+!   ortho_eps = 1d-11
 /
 &IONS
     ion_dynamics = 'verlet'

executables/deepmd/dp.yml

@@ -0,0 +1,13 @@
+isDefault: false
+monitors:
+  - standard_output
+results: []
+flavors:
+  dp_train_se_e2_r:
+    input:
+      - name: dp_train_se_e2_r.json
+    results: []
+    monitors:
+      - standard_output
+    applicationName: deepmd
+    executableName: dp  # dp train dp_train_se_e2_r.json && dp freeze -o graph.pb

executables/deepmd/lmp.yml

@@ -0,0 +1,13 @@
+isDefault: false
+monitors:
+  - standard_output
+results: []
+flavors:
+  lammps_md:
+    input:
+      - name: in.lammps
+    results: []
+    monitors:
+      - standard_output
+    applicationName: deepmd
+    executableName: lmp  # mpirun -np $NP lmp -in in.lammps

executables/deepmd/python.yml

@@ -0,0 +1,24 @@
+isDefault: true
+monitors:
+  - standard_output
+results: []
+flavors:
+  espresso_cp_to_deepmd:
+    isDefault: true
+    input:
+      - name: espresso_cp_to_deepmd.py
+    results: []
+    monitors:
+      - standard_output
+    applicationName: deepmd
+    executableName: python
+
+  espresso_to_lammps_structure:
+    isDefault: false
+    input:
+      - name: espresso_to_lammps_structure.py
+    results: []
+    monitors:
+      - standard_output
+    applicationName: deepmd
+    executableName: python

executables/espresso/cp.x.yml

@@ -3,6 +3,7 @@ monitors:
 results: []
 flavors:
   cp:
+    isDefault: true
     input:
       - name: cp.in
     results: []

executables/tree.yml

@@ -1,3 +1,7 @@
+deepmd:
+  dp: !include 'executables/deepmd/dp.yml'
+  lmp: !include 'executables/deepmd/lmp.yml'
+  python: !include 'executables/deepmd/python.yml'
 espresso:
   average.x: !include 'executables/espresso/average.x.yml'
   bands.x: !include 'executables/espresso/bands.x.yml'

src/js/index.js

@@ -11,6 +11,7 @@ export const allApplications = [
     "espresso",
     "jupyterLab",
     "exabyteml",
+    "deepmd",
     "nwchem",
     "python",
     "shell",

templates/deepmd/dp_create_lmp_structure.py.yml

@@ -0,0 +1,5 @@
+- content: !readFile 'assets/deepmd/espresso_to_lammps_structure.j2.py'
+  name: espresso_to_lammps_structure.py
+  contextProviders: []
+  applicationName: deepmd
+  executableName: python

templates/deepmd/dp_lmp.yml

@@ -0,0 +1,5 @@
+- content: !readFile 'assets/deepmd/in.lammps'
+  name: in.lammps
+  contextProviders: []
+  applicationName: deepmd
+  executableName: lmp

templates/deepmd/dp_prepare.py.yml

@@ -0,0 +1,5 @@
+- content: !readFile 'assets/deepmd/espresso_cp_to_deepmd.j2.py'
+  name: espresso_cp_to_deepmd.py
+  contextProviders: []
+  applicationName: deepmd
+  executableName: python

templates/deepmd/dp_train.yml

@@ -0,0 +1,5 @@
+- content: !readFile 'assets/deepmd/dp_train_se_e2_r.j2.json'
+  name: dp_train_se_e2_r.json
+  contextProviders: []
+  applicationName: deepmd
+  executableName: dp

templates/templates.yml

@@ -1,4 +1,10 @@
 !flatten
+# deepmd
+- !include 'templates/deepmd/dp_create_lmp_structure.py.yml'
+- !include 'templates/deepmd/dp_lmp.yml'
+- !include 'templates/deepmd/dp_prepare.py.yml'
+- !include 'templates/deepmd/dp_train.yml'
+# espresso
 - !include 'templates/espresso/average.x.yml'
 - !include 'templates/espresso/bands.x.yml'
 - !include 'templates/espresso/cp.x.yml'

tests/test.js

@@ -81,6 +81,18 @@ describe("assets for all executables", () => {
         templates = getAllAppTemplates();
     });
 
+    it("exists at least 1 asset for each tree entry for deepmd tree", () => {
+        const tree = APP_TREE.deepmd;
+
+        Object.keys(tree).forEach((treeItemName) => {
+            const treeItemTemplates = templates.filter(
+                (template) => template.executableName === treeItemName,
+            );
+
+            assert(treeItemTemplates.length > 0);
+        });
+    });
+
     it("exists at least 1 asset for each tree entry for espresso tree", () => {
         const tree = APP_TREE.espresso;