Merge pull request #31 from Humourist/fluctuated_water_FF

Fluctuated leading term water force field

Author: KuangYu

dmff/admp/pairwise.py

@@ -40,6 +40,9 @@ def distribute_multipoles(multipoles, index):
 def distribute_dispcoeff(c_list, index):
     return c_list[index]
 
+@jit_condition(static_argnums=())
+def distribute_matrix(multipoles,index1,index2):
+    return multipoles[index1,index2]
 
 def generate_pairwise_interaction(pair_int_kernel, covalent_map, static_args):
     '''

dmff/admp/parser.py

@@ -3,6 +3,8 @@
 import numpy as np
 import warnings
 from collections import defaultdict
+import jax.numpy as jnp
+from dmff.admp.multipole import convert_cart2harm
 
 def read_atom_line(line_full):
     """
@@ -326,7 +328,8 @@ def read_xml(fileobj):
     set_axis_type(atomTemplates)
 
     return atomTemplates, residueTemplates
-        
+
+
 class Atom:
 
     def __init__(self, serial, name, resName, resSeq, position, charge, ) -> None:
@@ -474,4 +477,4 @@ def assemble_covalent(residueDicts, natoms):
                 covalent_map[c][pp] = dr
 
     return covalent_map
-    
+   

dmff/admp/pme.py

@@ -27,7 +27,8 @@
 from dmff.admp.pairwise import (
     distribute_scalar, 
     distribute_v3, 
-    distribute_multipoles
+    distribute_multipoles,
+    distribute_matrix
 )
 
 
@@ -792,7 +793,8 @@ def pme_real(positions, box, pairs,
     r2 = distribute_v3(positions, pairs[:, 1])
     Q_extendi = distribute_multipoles(Q_global, pairs[:, 0])
     Q_extendj = distribute_multipoles(Q_global, pairs[:, 1])
-    nbonds = covalent_map[pairs[:, 0], pairs[:, 1]]
+    nbonds = distribute_matrix(covalent_map,pairs[:, 0],pairs[:, 1])
+    #nbonds = covalent_map[pairs[:, 0], pairs[:, 1]]
     indices = nbonds-1
     mscales = distribute_scalar(mScales, indices)
     mscales = mscales * buffer_scales
@@ -896,4 +898,4 @@ def pol_penalty(U_ind, pol):
     # this is to remove the singularity when pol=0
     pol_pi = trim_val_0(pol)
     # pol_pi = pol/(jnp.exp((-pol+1e-08)*1e10)+1) + 1e-08/(jnp.exp((pol-1e-08)*1e10)+1)
-    return jnp.sum(0.5/pol_pi*(U_ind**2).T) * DIELECTRIC
+    return jnp.sum(0.5/pol_pi*(U_ind**2).T) * DIELECTRIC

dmff/api.py

@@ -203,7 +203,6 @@ def createForce(self, system, data, nonbondedMethod, nonbondedCutoff, args):
         self.map_atomtype = map_atomtype
         # build covalent map
         covalent_map = build_covalent_map(data, 6)
-
         # here box is only used to setup ewald parameters, no need to be differentiable
         a, b, c = system.getDefaultPeriodicBoxVectors()
         box = jnp.array([a._value, b._value, c._value]) * 10