From 96f0a82aa5ad030da3d432ab106ffd9416077ed1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 17 May 2017 07:48:15 -0400
Subject: [PATCH] simplify class names in pair style python examples. add SPC/E
water example
---
examples/python/in.pair_python_hybrid | 2 +-
examples/python/in.pair_python_melt | 2 +-
examples/python/in.pair_python_spce | 28 ++++++++++++++++++
examples/python/potentials.py | 41 ++++++++++++++++++++++++++-
4 files changed, 70 insertions(+), 3 deletions(-)
create mode 100644 examples/python/in.pair_python_spce
diff --git a/examples/python/in.pair_python_hybrid b/examples/python/in.pair_python_hybrid
index b917910a29..dcd1f1e35c 100644
--- a/examples/python/in.pair_python_hybrid
+++ b/examples/python/in.pair_python_hybrid
@@ -12,7 +12,7 @@ mass * 1.0
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
-pair_coeff * * python potentials.LAMMPSLJCutPotential lj NULL
+pair_coeff * * python potentials.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
diff --git a/examples/python/in.pair_python_melt b/examples/python/in.pair_python_melt
index 2367ea0026..2349f080d4 100644
--- a/examples/python/in.pair_python_melt
+++ b/examples/python/in.pair_python_melt
@@ -12,7 +12,7 @@ mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
-pair_coeff * * potentials.LAMMPSLJCutPotential lj
+pair_coeff * * potentials.LJCutMelt lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
diff --git a/examples/python/in.pair_python_spce b/examples/python/in.pair_python_spce
new file mode 100644
index 0000000000..d3765ebc33
--- /dev/null
+++ b/examples/python/in.pair_python_spce
@@ -0,0 +1,28 @@
+units real
+atom_style full
+
+read_data data.spce
+
+pair_style hybrid/overlay python 12.0 coul/long 12.0
+kspace_style pppm 1.0e-6
+
+pair_coeff * * coul/long
+pair_coeff * * python potentials.LJCutSPCE OW NULL
+
+bond_style harmonic
+angle_style harmonic
+dihedral_style none
+improper_style none
+
+bond_coeff 1 1000.00 1.000
+angle_coeff 1 100.0 109.47
+
+special_bonds lj/coul 0.0 0.0 1.0
+
+neighbor 2.0 bin
+
+fix 1 all shake 0.0001 20 0 b 1 a 1
+fix 2 all nvt temp 300.0 300.0 100.0
+
+thermo 10
+run 100
diff --git a/examples/python/potentials.py b/examples/python/potentials.py
index 2438a8ba46..dbce8cd445 100644
--- a/examples/python/potentials.py
+++ b/examples/python/potentials.py
@@ -1,6 +1,6 @@
from __future__ import print_function
-class LAMMPSLJCutPotential(object):
+class LJCutMelt(object):
def __init__(self):
self.pmap=dict()
@@ -32,3 +32,42 @@ class LAMMPSLJCutPotential(object):
lj3 = coeff[4]
lj4 = coeff[5]
return (r6inv * (lj3*r6inv - lj4))
+
+class LJCutSPCE(object):
+
+ def __init__(self):
+ self.pmap=dict()
+ # SPCE oxygen in real units
+ eps=0.15535
+ sig=3.166
+
+ # set coeffs: eps, sig, 48*eps*sig**12, 24*eps*sig**6,
+ # 4*eps*sig**12, 4*eps*sig**6
+ self.coeff = {'OW' : {'OW' : (1.0,1.0,
+ 48.0*eps*sig**12,24.0*eps*sig**6,
+ 4.0*eps*sig**12, 4.0*eps*sig**6),
+ 'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)},
+ 'NULL': {'OW' : (0.0,1.0, 0.0, 0.0,0.0,0.0),
+ 'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)}}
+
+ def map_coeff(self,name,type):
+ if name in self.coeff:
+ self.pmap[type] = name
+ else:
+ raise Exception("cannot match atom type %s" % name)
+
+ def compute_force(self,rsq,itype,jtype):
+ coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
+ r2inv = 1.0/rsq
+ r6inv = r2inv*r2inv*r2inv
+ lj1 = coeff[2]
+ lj2 = coeff[3]
+ return (r6inv * (lj1*r6inv - lj2))
+
+ def compute_energy(self,rsq,itype,jtype):
+ coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
+ r2inv = 1.0/rsq
+ r6inv = r2inv*r2inv*r2inv
+ lj3 = coeff[4]
+ lj4 = coeff[5]
+ return (r6inv * (lj3*r6inv - lj4))
--
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