diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 341483d7a7231ef39ca2595ce5d2c4aa6d3d4ac7..0e4b6037c153fa3c32e7d82d2a3475fde6e95ee0 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -1153,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@@ -1610,11 +1610,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
in this format. See src/USER-NC-DUMP/README for more details.
NetCDF files can be directly visualized with the following tools:
+
Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
- and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
- a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
The person who created these files is Lars Pastewka at
Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index ee122e0a7266fbef10658d6d30552675b0a6ea75..da693a1b956fff65d28055c5961c6e1e4600e780 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0 :pre
-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes. The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes. The {CPU use} line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.
The MPI task section gives the breakdown of the CPU run time (in
seconds) into major categories:
@@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
addition, when using {timer full} and the "package omp"_package.html
command are active, a similar timing summary of time spent in threaded
regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
reducing the per-thread data elements to the storage for non-threaded
computation. These thread timings are taking from the first MPI rank
only and and thus, as the breakdown for MPI tasks can change from MPI
diff --git a/doc/src/commands.txt b/doc/src/commands.txt
index c5f22c666f92686341fe9b4446e1abd3c792ee47..2fdb69ea4de09c23e62c3da78ab1367fb34618ca 100644
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@@ -91,6 +91,7 @@ Commands :h1
suffix
tad
temper
+ temper_grem
thermo
thermo_modify
thermo_style
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index e7e54a6b3be9ef0bf39092ad8c2c2c6003d8500b..1d01798791ad4db5c21d3cc3c4c6953e849b4df1 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -35,6 +35,7 @@ Computes :h1
compute_erotate_sphere_atom
compute_event_displace
compute_fep
+ compute_global_atom
compute_group_group
compute_gyration
compute_gyration_chunk
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index eac4d6f4bacd0ad5b1736d5b00f995bb94f6d017..3fc5c1a10e8a1299d11dbf6fbabe4ab1f1509a34 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -29,7 +29,7 @@ fix fxgREM all grem 502 -0.15 -80000 fxnvt :pre
[Description:]
This fix implements the molecular dynamics version of the generalized
-replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,
which uses non-Boltzmann ensembles to sample over first order phase
transitions. The is done by defining replicas with an enthalpy
dependent effective temperature
@@ -103,7 +103,7 @@ npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
:line
-:link(Kim)
+:link(Kim2010)
[(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
:link(Malolepsza)
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 307b182fe2ad483bf88e666a60535ffcc59bbe1b..c4834dbbda702064edd6dbcb3ad8179bf477bfe6 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -23,6 +23,7 @@ Section_history.html
tutorial_drude.html
tutorial_github.html
+tutorial_pylammps.html
body.html
manifolds.html
@@ -113,6 +114,7 @@ special_bonds.html
suffix.html
tad.html
temper.html
+temper_grem.html
thermo.html
thermo_modify.html
thermo_style.html
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index b41bbdf020f78cc4fc2cadba47a12d8f5e093a1f..6145c8704cc131b96d21464031c9697733be02d1 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -32,7 +32,7 @@ Run a parallel tempering or replica exchange simulation in LAMMPS
partition mode using multiple generalized replicas (ensembles) of a
system defined by "fix grem"_fix_grem.html, which stands for the
generalized replica exchange method (gREM) originally developed by
-"(Kim)"_#Kim. It uses non-Boltzmann ensembles to sample over first
+"(Kim)"_#KimStraub. It uses non-Boltzmann ensembles to sample over first
order phase transitions. The is done by defining replicas with an
enthalpy dependent effective temperature
@@ -105,5 +105,5 @@ This command must be used with "fix grem"_fix_grem.html.
[Default:] none
-:link(Kim)
+:link(KimStraub)
[(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index c37798cff3ef3bcd5e6863c3c79dd88131fa446d..358ec75a53ecc6d29c90e0e58075690e5ba76141 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -33,14 +33,14 @@ timer loop :pre
Select the level of detail at which LAMMPS performs its CPU timings.
Multiple keywords can be specified with the {timer} command. For
keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.
During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.
The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time for a run and not collect any
@@ -52,20 +52,22 @@ procsessors. The {full} setting adds information about CPU
utilization and thread utilization, when multi-threading is enabled.
With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
-slow down the simulation. Using the {nosync} setting (which is the
-default) turns off this synchronization.
+call which measures load imbalance for each section more accuractly,
+though it can also slow down the simulation by prohibiting overlapping
+independent computations on different MPI ranks Using the {nosync}
+setting (which is the default) turns this synchronization off.
-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
-e.g. when running under a batch system and you want to maximize
-the utilization of the batch time slot, especially when the time
-per timestep varies and is thus difficult to predict how many
-steps a simulation can perform, or for difficult to converge
-minimizations. The timeout {elapse} value should be somewhat smaller
-than the time requested from the batch system, as there is usually
-some overhead to launch jobs, and it may be advisable to write
+This can be convenient when calculations have to comply with execution
+time limits, e.g. when running under a batch system when you want to
+maximize the utilization of the batch time slot, especially for runs
+where the time per timestep varies much and thus it becomes difficult
+to predict how many steps a simulation can perform for a given walltime
+limit. This also applies for difficult to converge minimizations.
+The timeout {elapse} value should be somewhat smaller than the maximum
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
out a restart after terminating a run due to a timeout.
The timeout timer starts when the command is issued. When the time
diff --git a/src/.gitignore b/src/.gitignore
index 6290aa9259d7f8b02daba6b666d077290ece9218..ff139216bb016f626af63ab32f68cb241f1a67f9 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -374,6 +374,8 @@
/fix_meso.h
/fix_meso_stationary.cpp
/fix_meso_stationary.h
+/fix_mscg.cpp
+/fix_mscg.h
/fix_msst.cpp
/fix_msst.h
/fix_neb.cpp
@@ -394,6 +396,8 @@
/fix_nph_body.h
/fix_npt_body.cpp
/fix_npt_body.h
+/fix_nvk.cpp
+/fix_nvk.h
/fix_nvt_body.cpp
/fix_nvt_body.h
/fix_nve_body.cpp
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index e8baca759dc2f247c68365e3380a1406d93b0dc9..c4e03a24a97609d6dffd22e43a72f3aea8b5b0f9 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -47,9 +47,9 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), radius_poly(NULL), frac_poly(NULL),
- idrigid(NULL), idshake(NULL), onemols(NULL), molfrac(NULL), coords(NULL),
- imageflags(NULL), fixrigid(NULL), fixshake(NULL), recvcounts(NULL),
+ Fix(lmp, narg, arg), radius_poly(NULL), frac_poly(NULL),
+ idrigid(NULL), idshake(NULL), onemols(NULL), molfrac(NULL), coords(NULL),
+ imageflags(NULL), fixrigid(NULL), fixshake(NULL), recvcounts(NULL),
displs(NULL), random(NULL), random2(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal fix pour command");
@@ -545,7 +545,7 @@ void FixPour::pre_exchange()
delx = coords[m][0] - xnear[i][0];
dely = coords[m][1] - xnear[i][1];
delz = coords[m][2] - xnear[i][2];
- domain->minimum_image(delx,dely,delz);
+ domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
radsum = coords[m][3] + xnear[i][3];
if (rsq <= radsum*radsum) break;
@@ -650,10 +650,10 @@ void FixPour::pre_exchange()
atom->radius[n] = radtmp;
atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp;
} else {
- onemols[imol]->quat_external = quat;
- atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
- }
-
+ onemols[imol]->quat_external = quat;
+ atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
+ }
+
modify->create_attribute(n);
}
}
@@ -1006,7 +1006,7 @@ void FixPour::options(int narg, char **arg)
vxhi = force->numeric(FLERR,arg[iarg+2]);
vylo = force->numeric(FLERR,arg[iarg+3]);
vyhi = force->numeric(FLERR,arg[iarg+4]);
- if (vxlo > vxhi || vylo > vyhi)
+ if (vxlo > vxhi || vylo > vyhi)
error->all(FLERR,"Illegal fix pour command");
vz = force->numeric(FLERR,arg[iarg+5]);
iarg += 6;
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 05933fd57c9aef9bf9e581582981ebd7d1c9221e..eeec94fdf729a76694188a715119781adfaaefe5 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -149,7 +149,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = ZCYLINDER;
lo = hi = 0.0;
- cylradius = force->numeric(FLERR,arg[iarg+3]);
+ cylradius = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index 8283c09110bf828474dfebded3ca949de4c1e317..d56715230a21c854a5ce6c7421d74769c7e6158f 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -44,7 +44,7 @@ enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,BONDED_HISTORY};
/* ---------------------------------------------------------------------- */
FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) :
- FixWallGran(lmp, narg, arg), region(NULL), region_style(NULL), ncontact(NULL),
+ FixWallGran(lmp, narg, arg), region(NULL), region_style(NULL), ncontact(NULL),
walls(NULL), shearmany(NULL), c2r(NULL)
{
restart_global = 1;
@@ -57,13 +57,13 @@ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) :
region_style = new char[strlen(region->style)+1];
strcpy(region_style,region->style);
nregion = region->nregion;
-
+
tmax = domain->regions[iregion]->tmax;
c2r = new int[tmax];
// re-allocate atom-based arrays with nshear
// do not register with Atom class, since parent class did that
-
+
memory->destroy(shearone);
shearone = NULL;
@@ -71,7 +71,7 @@ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) :
walls = NULL;
shearmany = NULL;
grow_arrays(atom->nmax);
-
+
// initialize shear history as if particle is not touching region
if (history) {
@@ -117,7 +117,7 @@ void FixWallGranRegion::init()
region->reset_vel();
}
- if (motion_resetflag){
+ if (motion_resetflag){
char str[256];
sprintf(str,"Region properties for region %s are inconsistent "
"with restart file, resetting its motion",idregion);
@@ -180,15 +180,15 @@ void FixWallGranRegion::post_force(int vflag)
if (regiondynamic) {
region->prematch();
- region->set_velocity();
+ region->set_velocity();
}
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) continue;
-
+
nc = region->surface(x[i][0],x[i][1],x[i][2],radius[i]);
- if (nc > tmax)
+ if (nc > tmax)
error->one(FLERR,"Too many wall/gran/region contacts for one particle");
// shear history maintenance
@@ -210,7 +210,7 @@ void FixWallGranRegion::post_force(int vflag)
walls[i][0] = iwall;
for (m = 0; m < sheardim; m++)
shearmany[i][0][m] = 0.0;
- } else if (ncontact[i] > 1 || iwall != walls[i][0])
+ } else if (ncontact[i] > 1 || iwall != walls[i][0])
update_contacts(i,nc);
} else update_contacts(i,nc);
}
@@ -233,12 +233,12 @@ void FixWallGranRegion::post_force(int vflag)
// meff = effective mass of sphere
// if I is part of rigid body, use body mass
-
+
meff = rmass[i];
if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
// invoke sphere/wall interaction
-
+
if (pairstyle == HOOKE)
hooke(rsq,dx,dy,dz,vwall,v[i],f[i],
omega[i],torque[i],radius[i],meff);
@@ -453,11 +453,11 @@ void FixWallGranRegion::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
-
+
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
-
+
int count = ncontact[nlocal] = (int) ubuf(extra[nlocal][m++]).i;
for (int iwall = 0; iwall < count; iwall++) {
walls[nlocal][iwall] = (int) ubuf(extra[nlocal][m++]).i;
@@ -506,5 +506,5 @@ void FixWallGranRegion::write_restart(FILE *fp)
void FixWallGranRegion::restart(char *buf)
{
int n = 0;
- if (!region->restart(buf,n)) motion_resetflag = 1;
+ if (!region->restart(buf,n)) motion_resetflag = 1;
}
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index 6504af57d92a71705023a488fa9ef14035b507c1..eb311fe3dba3daaadfb6f0223fea89c56df653f7 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -51,6 +51,8 @@ PairBuckLongCoulLong::PairBuckLongCoulLong(LAMMPS *lmp) : Pair(lmp)
dispersionflag = ewaldflag = pppmflag = 1;
respa_enable = 1;
writedata = 1;
+ ftable = NULL;
+ fdisptable = NULL;
}
/* ----------------------------------------------------------------------
@@ -230,7 +232,27 @@ void PairBuckLongCoulLong::init_style()
// require an atom style with charge defined
if (!atom->q_flag && (ewald_order&(1<<1)))
- error->all(FLERR,"Pair style buck/long/coul/long requires atom attribute q");
+ error->all(FLERR,
+ "Invoking coulombic in pair style buck/long/coul/long requires atom attribute q");
+
+ // ensure use of KSpace long-range solver, set two g_ewalds
+
+ if (force->kspace == NULL)
+ error->all(FLERR,"Pair style requires a KSpace style");
+ if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
+ if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
+
+ // set rRESPA cutoffs
+
+ if (strstr(update->integrate_style,"respa") &&
+ ((Respa *) update->integrate)->level_inner >= 0)
+ cut_respa = ((Respa *) update->integrate)->cutoff;
+ else cut_respa = NULL;
+
+ // setup force tables
+
+ if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
+ if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_buck_global);
// request regular or rRESPA neighbor lists if neighrequest_flag != 0
@@ -271,24 +293,6 @@ void PairBuckLongCoulLong::init_style()
}
cut_coulsq = cut_coul * cut_coul;
-
- // set rRESPA cutoffs
-
- if (strstr(update->integrate_style,"respa") &&
- ((Respa *) update->integrate)->level_inner >= 0)
- cut_respa = ((Respa *) update->integrate)->cutoff;
- else cut_respa = NULL;
-
- // ensure use of KSpace long-range solver, set two g_ewalds
-
- if (force->kspace == NULL)
- error->all(FLERR,"Pair style requires a KSpace style");
- if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
- if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
- // setup force tables
-
- if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
- if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_buck_global);
}
/* ----------------------------------------------------------------------
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index 5ae607a2f055471cb5eb22be454ed5fa6a6fdfa8..90d517ca288f625859f26415734e754a7b08d0c9 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -81,10 +81,12 @@ void PairLJLongCoulLong::settings(int narg, char **arg)
{
if (narg != 3 && narg != 4) error->all(FLERR,"Illegal pair_style command");
- ewald_off = 0;
ewald_order = 0;
- options(arg, 6);
- options(++arg, 1);
+ ewald_off = 0;
+
+ options(arg,6);
+ options(++arg,1);
+
if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
error->warning(FLERR,"Using largest cutoff for lj/long/coul/long");
if (!*(++arg))
@@ -226,7 +228,26 @@ void PairLJLongCoulLong::init_style()
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(FLERR,
- "Invoking coulombic in pair style lj/coul requires atom attribute q");
+ "Invoking coulombic in pair style lj/long/coul/long requires atom attribute q");
+
+ // ensure use of KSpace long-range solver, set two g_ewalds
+
+ if (force->kspace == NULL)
+ error->all(FLERR,"Pair style requires a KSpace style");
+ if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
+ if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
+
+ // set rRESPA cutoffs
+
+ if (strstr(update->integrate_style,"respa") &&
+ ((Respa *) update->integrate)->level_inner >= 0)
+ cut_respa = ((Respa *) update->integrate)->cutoff;
+ else cut_respa = NULL;
+
+ // setup force tables
+
+ if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
+ if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_lj_global);
// request regular or rRESPA neighbor lists if neighrequest_flag != 0
@@ -265,27 +286,8 @@ void PairLJLongCoulLong::init_style()
} else irequest = neighbor->request(this,instance_me);
}
- cut_coulsq = cut_coul * cut_coul;
-
- // set rRESPA cutoffs
-
- if (strstr(update->integrate_style,"respa") &&
- ((Respa *) update->integrate)->level_inner >= 0)
- cut_respa = ((Respa *) update->integrate)->cutoff;
- else cut_respa = NULL;
-
- // ensure use of KSpace long-range solver, set g_ewald
-
- if (force->kspace == NULL)
- error->all(FLERR,"Pair style requires a KSpace style");
- if (force->kspace) g_ewald = force->kspace->g_ewald;
- if (force->kspace) g_ewald_6 = force->kspace->g_ewald_6;
-
- // setup force tables
-
- if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
- if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_lj_global);
+ cut_coulsq = cut_coul * cut_coul;
}
/* ----------------------------------------------------------------------
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu
index b34ff47761192433e3adc74007620e3c6ba4f6cf..b7db0645740a1fa62db80bc4e3637500af7f9fce 100755
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu
@@ -54,7 +54,7 @@ MPI_LIB =
FFT_INC = -DFFT_MKL -DFFT_SINGLE
FFT_PATH =
-FFT_LIB = -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
-lmkl_sequential -lmkl_core
# JPEG and/or PNG library
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
index 74ff65d0c3ef9ce309e1591d947ed63d02c7b2ff..2cb37ed9fed4d36207ac86052a26f6d1b9cea4c1 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
@@ -54,7 +54,7 @@ MPI_LIB =
FFT_INC = -DFFT_MKL -DFFT_SINGLE
FFT_PATH =
-FFT_LIB = -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
-lmkl_sequential -lmkl_core
# JPEG and/or PNG library
diff --git a/src/MAKE/OPTIONS/Makefile.knl b/src/MAKE/OPTIONS/Makefile.knl
index 1260a27a124c57eaf1eb4561270293e9501b32e1..3bc777592e0164b4d5df1cd6eb0e95bca210d705 100644
--- a/src/MAKE/OPTIONS/Makefile.knl
+++ b/src/MAKE/OPTIONS/Makefile.knl
@@ -54,7 +54,7 @@ MPI_LIB =
FFT_INC = -DFFT_MKL -DFFT_SINGLE
FFT_PATH =
-FFT_LIB = -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
-lmkl_sequential -lmkl_core
# JPEG and/or PNG library
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index fafcf7aee376d6d2fb2ea345e349c5508b6c96e7..925c5fbf81ff1c6340670bf00b8abf34044a9091 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -493,7 +493,7 @@ ComputeChunkAtom::~ComputeChunkAtom()
{
// check nfix in case all fixes have already been deleted
- if (modify->nfix) modify->delete_fix(id_fix);
+ if (id_fix && modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
memory->destroy(chunk);
diff --git a/src/finish.cpp b/src/finish.cpp
index 9222d4e868f9661977f93a85145bc195e7cf595e..015ac46cac42189306ca508152cf52b0309ee958 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -247,7 +247,7 @@ void Finish::end(int flag)
}
}
- // PRD stats using PAIR,BOND,KSPACE for dephase,dynamics,quench
+ // PRD stats
if (prdflag) {
if (me == 0) {
@@ -329,7 +329,7 @@ void Finish::end(int flag)
}
}
- // TAD stats using PAIR,BOND,KSPACE for neb,dynamics,quench
+ // TAD stats
if (tadflag) {
if (me == 0) {
@@ -415,7 +415,7 @@ void Finish::end(int flag)
}
}
- // HYPER stats using PAIR,BOND,KSPACE for dynamics,quench
+ // HYPER stats
if (hyperflag) {
if (me == 0) {
@@ -912,7 +912,7 @@ void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt,
time_cpu = tmp/nprocs*100.0;
// % variance from the average as measure of load imbalance
- if ((time_sq/time - time) > 1.0e-10)
+ if ((time > 0.001) && ((time_sq/time - time) > 1.0e-10))
time_sq = sqrt(time_sq/time - time)*100.0;
else
time_sq = 0.0;
@@ -964,7 +964,7 @@ void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which,
time_std /= nthreads;
time_total /= nthreads;
- if ((time_std/time_avg -time_avg) > 1.0e-10)
+ if ((time_avg > 0.001) && ((time_std/time_avg -time_avg) > 1.0e-10))
time_std = sqrt(time_std/time_avg - time_avg)*100.0;
else
time_std = 0.0;
diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index 17b4b817aff5d8f058727e39a33eff779817a8f7..0693c0a0ff0df53f76f18336c69e2e706f0bd008 100755
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -43,10 +43,10 @@
# General Many thanks to Paul S. Crozier for checking script validity
# against his projects.
# Also thanks to Xiaohu Hu (hux2@ornl.gov) and Robert A. Latour
-# (latourr@clemson.edu), David Hyde-Volpe, and Tigran Abramyan,
-# Clemson University and Chris Lorenz (chris.lorenz@kcl.ac.uk),
-# King's College London for their efforts to add CMAP sections,
-# which is implemented using the option flag "-cmap".
+# (latourr@clemson.edu), David Hyde-Volpe, and Tigran Abramyan,
+# Clemson University and Chris Lorenz (chris.lorenz@kcl.ac.uk),
+# King's College London for their efforts to add CMAP sections,
+# which is implemented using the option flag "-cmap".
# Initialization