Update 3.usage.md

deepmodeling · Nov 8, 2023 · cc0a726 · cc0a726
1 parent 25ef0dd
commit cc0a726
Showing 1 changed file with 37 additions and 26 deletions.
diff --git a/docs/user_guide/3.usage.md b/docs/user_guide/3.usage.md
@@ -21,10 +21,10 @@ In this example, `lig.pdb` is the PDB file containing atomic coordinates, and `l
 
 If you run this script in `examples/classical`, you will get the following output.
 ```
-<function HarmonicBondJaxGenerator.createForce.<locals>.potential_fn at 0x112504af0>
-<function HarmonicAngleJaxGenerator.createForce.<locals>.potential_fn at 0x1124cd820>
-<function PeriodicTorsionJaxGenerator.createForce.<locals>.potential_fn at 0x18509b790>
-<function NonbondJaxGenerator.createForce.<locals>.potential_fn at 0x18509baf0>
+<function HarmonicBondGenerator.createPotential.<locals>.potential_fn at 0x7fe6c3bd2280>
+<function HarmonicAngleGenerator.createPotential.<locals>.potential_fn at 0x7fe6c3bd2670>
+<function PeriodicTorsionGenerator.createPotential.<locals>.potential_fn at 0x7fe6c3c4a8b0>
+<function NonbondedGenerator.createPotential.<locals>.potential_fn at 0x7fe6c3bd8670>
 ```
 The force field parameters are stored as a Python dict in the Hamiltonian.
 ```python
@@ -50,11 +50,11 @@ Each generated function will read coordinates, box, pairs and force field parame
 ```python
 positions = jnp.array(pdb.getPositions(asNumpy=True).value_in_unit(unit.nanometer))
 box = jnp.array([
-    [ 1.0,  0.0,  0.0],
-    [ 0.0,  1.0,  0.0],
-    [ 0.0,  0.0,  1.0]
+    [10.0,  0.0,  0.0],
+    [ 0.0, 10.0,  0.0],
+    [ 0.0,  0.0, 10.0]
 ])
-nbList = NeighborList(box, rc=4)
+nbList = NeighborList(box, rcut=4, cov_map=potentials.meta["cov_map"])
 nbList.allocate(positions)
 pairs = nbList.pairs
 ```
@@ -66,7 +66,7 @@ nbfunc = potentials.dmff_potentials['NonbondedForce']
 nbene = nbfunc(positions, box, pairs, params)
 print(nbene)
 ```
-If everything works fine, you will get `-425.41412` as a result. In addition, you can also use `getPotentialFunc()` and `getParameters()` to obtain the whole potential energy function and force field parameter set, instead of seperated functions for different energy terms.
+If everything works fine, you will get `-425.40470` as a result. In addition, you can also use `getPotentialFunc()` and `getParameters()` to obtain the whole potential energy function and force field parameter set, instead of seperated functions for different energy terms.
 ```python
 efunc = potentials.getPotentialFunc()
 params = ff.getParameters()
@@ -75,7 +75,7 @@ totene = efunc(positions, box, pairs, params)
 
 ## 3.2 Compute forces
 Different from conventional programming frameworks, explicit definition of atomic force calculation functions are no longer needed. Instead, the forces can be evaluated in an automatic manner with `jax.grad`.
-```
+```python
 pos_grad_func = jax.grad(efunc, argnums=0)
 force = -pos_grad_func(positions, box, pairs, params)
 ```
@@ -85,22 +85,33 @@ Similarly, the derivative of energy with regard to force field parameters can al
 ```python
 param_grad_func = jax.grad(nbfunc, argnums=-1)
 pgrad = param_grad_func(positions, box, pairs, params)
-print(pgrad["NonbondedForce"]["charge"])
+print(pgrad["NonbondedForce"]["sigma"])
 ```
 
-```python
-[ 652.7753      55.108738   729.36115   -171.4929     502.70837
-  -44.917206   129.63994   -142.31796   -149.62088    453.21503
-   46.372574   140.15303    575.488      461.46902    294.4358
-  335.25153     27.828705   671.3637     390.8903     519.6835
-  220.51129    238.7695     229.97302    210.58838    231.8734
-  196.40994    237.08563     35.663574   457.76416     77.4798
-  256.54382    402.2121     611.9573     440.8465     -52.09662
-  421.86688    592.46265    237.98883    110.286194   150.65375
-  218.61087    240.20477   -211.85376    150.7331     310.89404
-  208.65228   -139.23026   -168.8883     114.3645       3.7261353
-  399.6282     298.28455    422.06445    526.18463    521.27563
-  575.85767    606.74744    394.40845    549.84033    556.4724
-  485.1427     512.1267     558.55896    560.4667     562.812
-  333.74194  ]
+```
+[ 1.12090099e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  7.57040892e+02  1.45521139e+03  0.00000000e+00  0.00000000e+00
+  6.78143151e+01  5.87935802e+01  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  4.97000516e+02
+  0.00000000e+00  0.00000000e+00  1.69941295e+01  0.00000000e+00
+  4.15689683e+02  1.07864961e+02 -1.05927404e+01 -3.34661347e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  1.95772900e+01
+  9.87994968e+01  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  5.21105110e+01  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  3.11528443e+01  5.66372398e+01  6.27484044e+02  0.00000000e+00
+  1.87121279e+02  0.00000000e+00  0.00000000e+00  1.16098707e+02
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  6.27866628e+01  5.10221034e+01
+  0.00000000e+00  0.00000000e+00  3.60011535e+01  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00]
 ```