diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index e6d44733e2544534b9f29a6cdfc9b61500687ccb..444e901a4035140f9c984f017644d8d89f9c34c1 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="20 Jun 2017 version">
+<META NAME="docnumber" CONTENT="23 Jun 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
-20 Jun 2017 version :c,h4
+23 Jun 2017 version :c,h4
Version info: :h4
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 66091f4973fa23eec67605fd2e61055e03a05971..6d27bb7076344adfd81ba2a0b7242c985a3eff02 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
individual components of the pressure tensor, to compute per-atom virial,
or with suffix kspace/pair styles of MSM, like OMP or GPU.
-The {fftbench} keyword applies only to PPPM. It is on by default. If
-this option is turned off, LAMMPS will not take the time at the end
-of a run to give FFT benchmark timings, and will finish a few seconds
-faster than it would if this option were on.
+The {fftbench} keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.
The {collective} keyword applies only to PPPM. It is set to {no} by
default, except on IBM BlueGene machines. If this option is set to
@@ -306,7 +306,7 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
-yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
+yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
order/disp = 7.
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 9c5973c7255e240b5da207e9458c770198cfed43..1e78607c084e6b4ac07bca1cc8ec39a5a6585d80 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -104,7 +104,15 @@ charmmfsw"_dihedral_charmm.html command. Eventually code from the new
styles will propagate into the related pair styles (e.g. implicit,
accelerator, free energy variants).
-The general CHARMM formulas are as follows
+NOTE: The newest CHARMM pair styles reset the Coulombic energy
+conversion factor used internally in the code, from the LAMMPS value
+to the CHARMM value, as if it were effectively a parameter of the
+force field. This is because the CHARMM code uses a slightly
+different value for the this conversion factor in "real
+units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
+332.06371. This is to enable more precise agreement by LAMMPS with
+the CHARMM force field energies and forces, when using one of these
+two CHARMM pair styles.
:c,image(Eqs/pair_charmm.jpg)
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index a9622b32fd877ab79c5d51b02d0ab46133c5bee3..985581cac8b227ad8ee3a75ec187ef13c985068b 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. These formulas are discussed in
"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.
+Also note, that in the code, all of these terms (except Elj) have a
+C/epsilon prefactor, the same as the Coulombic term in the LJ +
+Coulombic pair styles discussed "here"_pair_lj.html. C is an
+energy-conversion constant and epsilon is the dielectric constant
+which can be set by the "dielectric"_dielectric.html command. The
+same is true of the equations that follow for other dipole pair
+styles.
+
Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
pairs of particles that each have a charge and/or a point dipole
moment. In general, a shifted-force potential is a (sligthly) modified
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 6e17a9bbd7b0cc7fde788379910fea98979d7fa0..30d8ab64b60f086c89d328402aa0b2ba8c45c282 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -25,6 +25,7 @@
#include <string.h>
#include "pair_lj_charmmfsw_coul_long.h"
#include "atom.h"
+#include "update.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
@@ -61,6 +62,15 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
// short-range/long-range flag accessed by DihedralCharmmfsw
dihedflag = 1;
+
+ // switch qqr2e from LAMMPS value to CHARMM value
+
+ if (strcmp(update->unit_style,"real") == 0) {
+ if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real))
+ error->message(FLERR,"Switching to CHARMM coulomb energy"
+ " conversion constant");
+ force->qqr2e = force->qqr2e_charmm_real;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -87,6 +97,15 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong()
}
if (ftable) free_tables();
}
+
+ // switch qqr2e back from CHARMM value to LAMMPS value
+
+ if (update && strcmp(update->unit_style,"real") == 0) {
+ if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real))
+ error->message(FLERR,"Restoring original LAMMPS coulomb energy"
+ " conversion constant");
+ force->qqr2e = force->qqr2e_lammps_real;
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 1e34b06478440568a078bd2f655fe55d10dc1347..0d2159b671ddf84969954c78b809ebef065ea560 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -25,6 +25,7 @@
#include <string.h>
#include "pair_lj_charmmfsw_coul_charmmfsh.h"
#include "atom.h"
+#include "update.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
@@ -46,6 +47,15 @@ PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
// short-range/long-range flag accessed by DihedralCharmmfsw
dihedflag = 0;
+
+ // switch qqr2e from LAMMPS value to CHARMM value
+
+ if (strcmp(update->unit_style,"real") == 0) {
+ if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real))
+ error->message(FLERR,"Switching to CHARMM coulomb energy"
+ " conversion constant");
+ force->qqr2e = force->qqr2e_charmm_real;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -71,6 +81,15 @@ PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh()
memory->destroy(lj14_4);
}
}
+
+ // switch qqr2e back from CHARMM value to LAMMPS value
+
+ if (update && strcmp(update->unit_style,"real") == 0) {
+ if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real))
+ error->message(FLERR,"Restoring original LAMMPS coulomb energy"
+ " conversion constant");
+ force->qqr2e = force->qqr2e_lammps_real;
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/force.cpp b/src/force.cpp
index 3dd28cc7105ba2b09694ae23aa11ab339c115ad5..33e66304067d8c1257d486ed4df44bdf8c80b445 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -53,6 +53,8 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
special_extra = 0;
dielectric = 1.0;
+ qqr2e_lammps_real = 332.06371; // these constants are toggled
+ qqr2e_charmm_real = 332.0716; // by new CHARMM pair styles
pair = NULL;
bond = NULL;
diff --git a/src/force.h b/src/force.h
index f2d9abc7dd235db067bab708669e0ae5cd633f08..edaac1b5277196b8b9ff81536d6c354b58c81ab4 100644
--- a/src/force.h
+++ b/src/force.h
@@ -43,6 +43,9 @@ class Force : protected Pointers {
double femtosecond; // 1 femtosecond in native units
double qelectron; // 1 electron charge abs() in native units
+ double qqr2e_lammps_real; // different versions of this constant
+ double qqr2e_charmm_real; // used by new CHARMM pair styles
+
int newton,newton_pair,newton_bond; // Newton's 3rd law settings
class Pair *pair;
diff --git a/src/min.cpp b/src/min.cpp
index d308efb8486e0ecdbd5280e2bd476c1f21726844..af23629cad8eafefcaab22f5752ee8d87ea9014a 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -165,8 +165,8 @@ void Min::init()
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (comm->me == 0)
- error->warning(FLERR,
- "Resetting reneighboring criteria during minimization");
+ error->warning(FLERR, "Using 'neigh_modify every 1 delay 0 check"
+ " yes' setting during minimization");
}
neighbor->every = 1;
diff --git a/src/update.cpp b/src/update.cpp
index 5599dc6c88492ea2fcfdf8f61b44f71a8d11108f..e4c85dde73ee497a708c0af4003713364d90e85d 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -154,7 +154,7 @@ void Update::set_units(const char *style)
force->ftm2v = 1.0 / 48.88821291 / 48.88821291;
force->mv2d = 1.0 / 0.602214129;
force->nktv2p = 68568.415;
- force->qqr2e = 332.06371;
+ force->qqr2e = 332.06371; // see also force->qqr2d_lammps_real
force->qe2f = 23.060549;
force->vxmu2f = 1.4393264316e4;
force->xxt2kmu = 0.1;
diff --git a/src/version.h b/src/version.h
index c2cdc6afd6627eee4ef7f4f0cb36082f942d6c7e..07bfcc388580507cb8296e16ae189db8082871ea 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Jun 2017"
+#define LAMMPS_VERSION "23 Jun 2017"