From a2303e5a15b27a40bf82b03bb1d5bf9f0c3c2b69 Mon Sep 17 00:00:00 2001
From: sergeylishchuk <sergey.lishchuk@gmail.com>
Date: Thu, 26 Jul 2018 11:54:04 +0100
Subject: [PATCH] more changes to ATM source and doc file
---
doc/src/pair_atm.txt | 14 +++++++-------
src/MANYBODY/pair_atm.cpp | 40 +++++++++++++++++++++++++++++++--------
src/MANYBODY/pair_atm.h | 5 +++++
3 files changed, 44 insertions(+), 15 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index e442c32814..6453b02bf8 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -41,17 +41,17 @@ gamma3 are as shown in this diagram:
Note that for the interaction between a triplet of atoms I,J,K, there
is no "central" atom. The interaction is symmetric with respect to
-permutation of the three atoms. In fact, it is computed 3 times by
-the code with each of I,J,K being atom 1. Thus the nu value must be
-the same for all those permutations of the atom types of I,J,K as
-discussed below.
+permutation of the three atoms. Thus the nu value is
+the same for all those permutations of the atom types of I,J,K
+and needs to be specified only once, as discussed below.
The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-The potential for a triplet of atom is calculated only if all 3
-distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
+The potential is calculated if atoms J and K are in the
+"neighbor list"_neighbor.html of atom I
+and the distances between atoms satisfy rIJ rJK rKI > cutoff^3.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@@ -88,7 +88,7 @@ pair_coeff 2 3 4 0.1 :pre
Note that for a simulation with a single atom type, only a single
entry is required, e.g.
-pair_coeff 1 1 1 0.25 :per
+pair_coeff 1 1 1 0.25 :pre
For a simulation with two atom types, four pair_coeff commands will
specify all possible nu values:
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 2ba8912899..090a8352d5 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -91,8 +91,8 @@ void PairATM::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
- double cutoffsq = cut_global*cut_global;
-
+ double cutoff_sixth = cut_global*cut_global;
+ cutoff_sixth = cutoff_sixth*cutoff_sixth*cutoff_sixth;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -112,26 +112,32 @@ void PairATM::compute(int eflag, int vflag)
j = jlist[jj];
j &= NEIGHMASK;
rij[0] = x[j][0] - xi;
+ if (rij[0] < 0.0) continue;
rij[1] = x[j][1] - yi;
+ if (rij[0] == 0.0 and rij[1] < 0.0) continue;
rij[2] = x[j][2] - zi;
+ if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
- rik[0] = x[k][0] - xi;
- rik[1] = x[k][1] - yi;
- rik[2] = x[k][2] - zi;
- rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
-
rjk[0] = x[k][0] - x[j][0];
+ if (rjk[0] < 0.0) continue;
rjk[1] = x[k][1] - x[j][1];
+ if (rjk[0] == 0.0 and rjk[1] < 0.0) continue;
rjk[2] = x[k][2] - x[j][2];
+ if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ rik[0] = x[k][0] - xi;
+ rik[1] = x[k][1] - yi;
+ rik[2] = x[k][2] - zi;
+ rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
+
r6 = rij2*rik2*rjk2;
- if (r6 > cutoffsq) continue;
+ if (r6 > cutoff_sixth) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
@@ -228,6 +234,9 @@ void PairATM::coeff(int narg, char **arg)
void PairATM::init_style()
{
+ if (force->newton_pair == 0)
+ error->all(FLERR,"Pair style ATM requires newton pair on");
+
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
@@ -258,6 +267,21 @@ double PairATM::init_one(int i, int j)
proc 0 writes to restart file
------------------------------------------------------------------------- */
+//
+// PLEASE HELP!
+//
+// From the pair_hybrid documentation:
+//
+// "For the hybrid pair styles, the list of sub-styles and their respective
+// settings are written to binary restart files, so a pair_style command
+// does not need to specified in an input script that reads a restart file.
+// However, the coefficient information is not stored in the restart file.
+// Thus, pair_coeff commands need to be re-specified in the restart input
+// script."
+//
+// As a result, the function "PairATM::write_restart" is not called from
+// "pair_hybrid.cpp". What is the best way to deal with this problem?
+//
void PairATM::write_restart(FILE *fp)
{
write_restart_settings(fp);
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 45a6cda344..210351cfad 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -64,6 +64,11 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
+E: Pair style ATM requires newton pair on
+
+See the newton command. This is a restriction to use the ATM
+potential.
+
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
--
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