fix bug and change Example

Author: gengxingze

README.md

@@ -1,4 +1,4 @@
-___
+from sympy.physics.units import forcefrom sympy.physics.units import energy___
 # ABFML 
 
 ## 1. Introduction
@@ -27,6 +27,9 @@ To get started with ABFML, follow these steps to set up the environment and inst
 #   This installs ABFML from the local directory.
 ```
 ### 2.2 Installing ABFML-LAMMPS
+In general for force field development users, this step can be skipped for now.
+It would be more efficient to apply it to large-scale molecular dynamics
+when all aspects of the force field are relevantly calculated/checked by the more convenient ASEs
 To integrate ABFML with LAMMPS, follow these steps:
 ```bash
 # 1. Download LAMMPS:
@@ -53,11 +56,18 @@ To integrate ABFML with LAMMPS, follow these steps:
    cd src
    make yes-abfml
    make mpi
+
+# 6. Run lammps:  
+   pair_style abfml model.pt
+   pair coeff * * 29 30
+  
+#   Use the element number to represent the element type
 ```
 **Note**: Ensure your GCC compiler is version 9.0 or above, as older versions may not support.
 
 ## 3. Build a new model
-Build your own model input in the input file and specify the path to the model's py file
+Build your own model input in the input file and specify the path to the model's py file,
+This is an example of a simple LJ potential, which can be found in example/new-model。
 ```json
 {
   "model_setting": {
@@ -72,7 +82,7 @@ Build your own model input in the input file and specify the path to the model's
   }
 }
 ```
-Then you can  use the relevant modules for training, validation and simulation
+Then you can use the relevant modules for training, validation and simulation
 
 ## 4. Run
 
@@ -84,15 +94,24 @@ To run an example using ABFML, follow these steps:
 # 2. Navigate to the example directory:
    cd abfml/example/dp
 
-# 3. Run:
+# 3. Quick check for model correctness
+   abfml check -m model.pt -d float32
+   
+# 4. train:
    abfml train input.json
 #   This command starts the training process using the configurations specified in `input.json`.
 
-# 4. Quick check for model correctness
-   abfml check -m model.pt -d float32
-# 5. Run lammps:  
-   pair_style abfml model.pt
-   pair coeff * * 29 30
-  
-#   Use the element number to represent the element type
+# 5. valid:
+   abfml valid -m 'model.pt' -f "../data/test.extxyz" -n 10
+```
+
+Use the ASE calculator to perform quick calculations on the model created.
+```python
+from abfml.calculate import ABFML
+from ase.build import bulk
+calc = ABFML('model.pt')
+structure = bulk('Cu', a=3.62)
+structure.calc = calc
+energy = structure.get_potential_energy()
+force = structure.get_forces()
 ```

abfml/entrypoints/check.py

@@ -19,7 +19,7 @@ def check_mlff(
         input: Optional[str] = None,
         dtype: str = "float32",
         **kwargs):
-    logger = Logger("valid.log").logger
+    logger = Logger("check.log").logger
     log_logo(logger=logger)
 
     if input is not None:
@@ -83,6 +83,26 @@ def check_mlff(
     logger.info(f"+----------------------------------------------------------------------------------------------+")
 
     logger.info(f"+-------------------------------------- periodicity check -------------------------------------+")
+    cluster = bulk('Cu', 'fcc', a=3.62, cubic=True)
+    cluster.calc = calculator
+    energy = [cluster.get_potential_energy()]
+    force = [cluster.get_forces()]
+    cluster = cluster * (3, 3, 3)
+    cluster.calc = calculator
+    energy.append(cluster.get_potential_energy())
+    force.append(cluster.get_forces())
+    dE = energy[1] - energy[0] * 27
+    dF = np.abs(force[1][:4] - force[0]).sum().item()
+    logger.info(f"       bulk-> energy: {energy[0]:>.6f}, force: {force[0].sum().item():>.6f}")
+    logger.info(f" 3*3*3 bulk-> energy: {energy[1]:>.6f}, force: {force[1].sum().item():>.6f}")
+    logger.info(f" difference-> E[1]-E[0]*27: {dE:>.6f},  dF: {dF:>.6f}")
+    logger.info(f"Information: The energy of the expanded cell of a periodic structure is proportional to the number")
+    logger.info(f"             of times it is expanded and the force on the corresponding atoms is unchanged.")
+    logger.warning(f"If the difference is less than 1e-5 it may be an accuracy problem,")
+    logger.warning(f"otherwise the energy and force relationship should be checked.")
+    logger.info(f"+----------------------------------------------------------------------------------------------+")
+
+    logger.info(f"+------------------------------------- energy-force check -------------------------------------+")
     cluster = Atoms(element_symbol + '3', position)
     cluster.calc = calculator
     energy = [cluster.get_potential_energy()]
@@ -100,22 +120,3 @@ def check_mlff(
     logger.warning(f"otherwise the energy and force relationship should be checked.")
     logger.info(f"+----------------------------------------------------------------------------------------------+")
 
-    logger.info(f"+------------------------------------- energy-force check -------------------------------------+")
-    cluster = bulk('Cu', 'fcc', a=3.62, cubic=True)
-    cluster.calc = calculator
-    energy = [cluster.get_potential_energy()]
-    force = [cluster.get_forces()]
-    cluster = cluster * (3,3,3)
-    cluster.calc = calculator
-    energy.append(cluster.get_potential_energy())
-    force.append(cluster.get_forces())
-    dE = energy[1] - energy[0] * 27
-    dF = np.abs(force[1][:4] - force[0]).sum().item()
-    logger.info(f"       bulk-> energy: {energy[0]:>.6f}, force: {force[0].sum().item():>.6f}")
-    logger.info(f" 3*3*3 bulk-> energy: {energy[1]:>.6f}, force: {force[1].sum().item():>.6f}")
-    logger.info(f" difference-> E[1]-E[0]*27: {dE:>.6f},  dF: {dF:>.6f}")
-    logger.info(f"Information: The energy of the expanded cell of a periodic structure is proportional to the number")
-    logger.info(f"             of times it is expanded and the force on the corresponding atoms is unchanged.")
-    logger.warning(f"If the difference is less than 1e-5 it may be an accuracy problem,")
-    logger.warning(f"otherwise the energy and force relationship should be checked.")
-    logger.info(f"+----------------------------------------------------------------------------------------------+")

abfml/model/normal.py

@@ -102,7 +102,7 @@ def normal(self, normal_loader, param_class: Param):
                                         torch.zeros(ntype, requires_grad=False)]
         from abfml.model.field_model_bp import BPMlp
         for i, image_batch in enumerate(normal_loader):
-            neighbor_list = image_batch['neighbor_list']
+            Nij= image_batch['Nij']
             Zij = image_batch['Zij']
             Rij = image_batch["Rij"]
             Zi = image_batch["Zi"]
@@ -112,7 +112,7 @@ def normal(self, normal_loader, param_class: Param):
                                             bp_features_information=param_class.BPDescriptor.bp_features_information,
                                             bp_features_param=param_class.BPDescriptor.bp_features_param,
                                             element_map=element_type,
-                                            neighbor_list=neighbor_list,
+                                            Nij=Nij,
                                             Zij=Zij,
                                             Rij=Rij)
 

example/bp-model/checkpoint_final.ckpt

@@ -42,8 +42,8 @@
 },
 "data_setting": {
                "file_format": "extxyz",
-               "train_file":  ["test1.extxyz"],
-               "valid_file":  ["test1.extxyz"]
+               "train_file":  ["../data/test.extxyz"],
+               "valid_file":  ["../data/test.extxyz"]
 },
 "train_setting": {
                "epoch": 1,

example/bp-model/bp_input.json renamed to example/bp-model/input.json

@@ -1,2 +1,2 @@
    Epoch       T_RMSE_Loss       V_RMSE_Loss      T_RMSE_E_tot      V_RMSE_E_tot      T_RMSE_Force      V_RMSE_Force      Total_Time(s)
-       1       3.25684e+00       4.03030e+00       1.28853e+00       1.22914e+00       1.96831e+00       1.53909e+00            0.08
+       1       2.37143e-01       1.71323e-01       9.88585e-02       2.08156e-02       1.38284e-01       7.51426e-02           56.81