diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 91052888ea32f9b75f69f8a155f46cee8ae734ba..0f6f8ec78b5a63d14358ea9693168860761845d0 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -732,7 +732,7 @@ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
:pre
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink", are created in lib/latte to point into the LATTE home dir.
+"filelink.o", are created in lib/latte to point into the LATTE home dir.
When LAMMPS builds in src it will use these links. You should
also check that the Makefile.lammps file you create is appropriate
for the compiler you use on your system to build LATTE.
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 0bc43a35cbf2b0c2f2a5e5e46e49eb075f1bfde0..5d18c39d994de3d58b752f7d595dfa4eb55e0019 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -138,17 +138,17 @@ By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word {end}, additional
forces can be applied to the first and/or last replicas, to enable
-them to relax toward a MEP while constraining their energy.
+them to relax toward a MEP while constraining their energy E to the
+target energy ETarget.
-The interatomic force Fi for the specified replica becomes:
+If ETarget>E, the interatomic force Fi for the specified replica becomes:
Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T', {when} Grad(V) dot T' < 0
Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
:pre
-where E is the current energy of the replica and ETarget is the target
-energy. The "spring" constant on the difference in energies is the
-specified {Kspring3} value.
+The "spring" constant on the difference in energies is the specified
+{Kspring3} value.
When {estyle} is specified as {first}, the force is applied to the
first replica. When {estyle} is specified as {last}, the force is
@@ -183,10 +183,9 @@ After converging a NEB calculation using an {estyle} of
have a larger energy than the first replica. If this is not the case,
the path is probably not a MEP.
-Finally, note that if the last replica converges toward a local
-minimum which has a larger energy than the energy of the first
-replica, a NEB calculation using an {estyle} of {last/efirst} or
-{last/efirst/middle} cannot reach final convergence.
+Finally, note that the last replica may never reach the target energy
+if it is stuck in a local minima which has a larger energy than the
+target energy.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index aef534ad25fcc1ea9e8d3aaddef04c9bd48a35e5..10bb89c94cad5b28414578f621cab34c31266165 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -111,6 +111,10 @@ need to communicate their new values to/from ghost atoms, an operation
that can be invoked from within a "pair style"_pair_style.html or
"fix"_fix.html or "compute"_compute.html that you write.
+NOTE: If this fix is defined [after] the simulation box is created,
+a 'run 0' command should be issued to properly initialize the storage
+created by this fix.
+
:line
This fix is one of a small number that can be defined in an input
@@ -155,7 +159,7 @@ these commands could be used:
fix prop all property/atom mol
variable cluster atom ((id-1)/10)+1
-set id * mol v_cluster :pre
+set atom * mol v_cluster :pre
The "atom-style variable"_variable.html will create values for atoms
with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
diff --git a/examples/python/funcs.py b/examples/python/funcs.py
index f38aca53f23ccabce6325987cea3065b6a7cda49..71865f62f46c9e2acc3f3bda2fa352eae3dc2fc1 100644
--- a/examples/python/funcs.py
+++ b/examples/python/funcs.py
@@ -8,17 +8,21 @@ def loop(N,cut0,thresh,lmpptr):
from lammps import lammps
lmp = lammps(ptr=lmpptr)
natoms = lmp.get_natoms()
-
- for i in range(N):
- cut = cut0 + i*0.1
- lmp.set_variable("cut",cut) # set a variable in LAMMPS
+ try:
+ for i in range(N):
+ cut = cut0 + i*0.1
- lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
- #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
+ lmp.set_variable("cut",cut) # set a variable in LAMMPS
+
+ lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
+ #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
+
+ lmp.command("pair_coeff * * 1.0 1.0") # ditto
+ lmp.command("run 10") # ditto
+ pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
+ print("PE",pe/natoms,thresh)
+ if pe/natoms < thresh: return
+ except Exception as e:
+ print("LOOP error:", e)
- lmp.command("pair_coeff * * 1.0 1.0") # ditto
- lmp.command("run 10") # ditto
- pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
- print("PE",pe/natoms,thresh)
- if pe/natoms < thresh: return
diff --git a/examples/python/in.python b/examples/python/in.python
index c5aa504d43159375715f293c6a27e5166f8b0d24..9372c684d664877ddb8aa3a99cb3a18172a7d249 100644
--- a/examples/python/in.python
+++ b/examples/python/in.python
@@ -28,6 +28,7 @@ python simple here """
from __future__ import print_function
def simple():
+ foo = 0
print("Inside simple function")
try:
foo += 1
diff --git a/lib/latte/README b/lib/latte/README
index bfa91e62cdead6bdbc1702995cc53a1bc1224ff5..bdf67dd59c1ca312a539628a10033b59b4f4e56b 100644
--- a/lib/latte/README
+++ b/lib/latte/README
@@ -28,14 +28,15 @@ Instructions:
and finally, build the code via the make command
% make
-3. Create three soft links in this dir (lib/latte)
+3. Create three symbolic links in this dir (lib/latte)
E.g if you built LATTE in this dir:
% ln -s ./LATTE-master/src includelink
% ln -s ./LATTE-master liblink
- % ln -s ./LATTE-master/src/latte_c_bind.o filelink
+ % ln -s ./LATTE-master/src/latte_c_bind.o filelink.o
4. Choose a Makefile.lammps.* file appropriate for your compiler
- (GNU gfortran or Intel ifort) and copy it to Makefile.lammps.
+ (GNU gfortran with external BLAS, GNU gfortran with local liblinalg,
+ or Intel ifort with MKL) and copy it to Makefile.lammps.
Note that you may need to edit Makefile.lammps for paths
and compiler options appropriate to your system.
@@ -49,7 +50,7 @@ with the LATTE package installed:
% make g++ (or whatever target you wish)
Note that if you download and unpack a new LAMMPS tarball, the
-"includelink" and "liblink" and "filelink" files will be lost and you
-will need to re-create them (step 3). If you built LATTE in this
-directory (as opposed to somewhere else on your system), you will also
-need to repeat steps 1,2,4.
+"includelink" and "liblink" and "filelink.o" symbolic links will be
+lost and you will need to re-create them (step 3). If you built LATTE
+in this directory (as opposed to somewhere else on your system), you
+will also need to repeat steps 1,2,4.
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index cf6e2814c0e0bb56f5a19b2a2481ea019259e114..03de42c68ca1d387784210e911d5cfe2f97c652d 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -969,6 +969,8 @@ void PPPMKokkos<DeviceType>::set_grid_global()
if (!gewaldflag) {
if (accuracy <= 0.0)
error->all(FLERR,"KSpace accuracy must be > 0");
+ if (q2 == 0.0)
+ error->all(FLERR,"Must use 'kspace_modify gewald' for uncharged system");
g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2);
if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
else g_ewald = sqrt(-log(g_ewald)) / cutoff;
@@ -1179,6 +1181,7 @@ double PPPMKokkos<DeviceType>::final_accuracy()
double yprd = domain->yprd;
double zprd = domain->zprd;
bigint natoms = atomKK->natoms;
+ if (natoms == 0) natoms = 1; // avoid division by zero
double df_kspace = compute_df_kspace();
double q2_over_sqrt = q2 / sqrt(natoms*cutoff*xprd*yprd*zprd);
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index d41443f02a1f669f4caa52477462dc68f60048b1..c7d242031f6d527455bbd2e78d0cdb761831ee98 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -154,6 +154,8 @@ void Ewald::init()
if (!gewaldflag) {
if (accuracy <= 0.0)
error->all(FLERR,"KSpace accuracy must be > 0");
+ if (q2 == 0.0)
+ error->all(FLERR,"Must use 'kspace_modify gewald' for uncharged system");
g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2);
if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
else g_ewald = sqrt(-log(g_ewald)) / cutoff;
@@ -340,6 +342,7 @@ void Ewald::setup()
double Ewald::rms(int km, double prd, bigint natoms, double q2)
{
+ if (natoms == 0) natoms = 1; // avoid division by zero
double value = 2.0*q2*g_ewald/prd *
sqrt(1.0/(MY_PI*km*natoms)) *
exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd));
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index 85e3da921b68b19154d96dcf871aba5399b63e28..e0424b0d932b7d4adbd50a5272695abe08da1fb9 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -193,6 +193,10 @@ void EwaldDisp::init()
if (!gewaldflag) {
if (function[0]) {
+ if (accuracy <= 0.0)
+ error->all(FLERR,"KSpace accuracy must be > 0");
+ if (q2 == 0.0)
+ error->all(FLERR,"Must use 'kspace_modify gewald' for uncharged system");
g_ewald = accuracy*sqrt(natoms*(*cutoff)*shape_det(domain->h)) / (2.0*q2);
if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/(*cutoff);
else g_ewald = sqrt(-log(g_ewald)) / (*cutoff);
@@ -298,6 +302,7 @@ double EwaldDisp::rms(int km, double prd, bigint natoms,
double q2, double b2, double M2)
{
double value = 0.0;
+ if (natoms == 0) natoms = 1; // avoid division by zero
// Coulombic
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 6add8b58b74dcf5a35ed1fd6cb1b8b75dda329d7..53ab2e5a9d72159e116e2cd02bba223552a558ca 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -1004,6 +1004,8 @@ void PPPM::set_grid_global()
if (!gewaldflag) {
if (accuracy <= 0.0)
error->all(FLERR,"KSpace accuracy must be > 0");
+ if (q2 == 0.0)
+ error->all(FLERR,"Must use kspace_modify gewald for uncharged system");
g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2);
if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
else g_ewald = sqrt(-log(g_ewald)) / cutoff;
@@ -1268,6 +1270,7 @@ double PPPM::compute_qopt()
double PPPM::estimate_ik_error(double h, double prd, bigint natoms)
{
double sum = 0.0;
+ if (natoms == 0) return 0.0;
for (int m = 0; m < order; m++)
sum += acons[order][m] * pow(h*g_ewald,2.0*m);
double value = q2 * pow(h*g_ewald,(double)order) *
@@ -1345,6 +1348,7 @@ double PPPM::final_accuracy()
double yprd = domain->yprd;
double zprd = domain->zprd;
bigint natoms = atom->natoms;
+ if (natoms == 0) natoms = 1; // avoid division by zero
double df_kspace = compute_df_kspace();
double q2_over_sqrt = q2 / sqrt(natoms*cutoff*xprd*yprd*zprd);
diff --git a/src/LATTE/README b/src/LATTE/README
index 2103074ad4524ca57e7ecd6dd3eb9d0a218a6672..d7379f2461847f943480ac6201b42b7e61f6b1a5 100644
--- a/src/LATTE/README
+++ b/src/LATTE/README
@@ -17,7 +17,7 @@ Once you have successfully built LAMMPS with this package and the
LATTE library you can test it using an input file from the examples
latte dir, e.g.
-lmp_serial < lammps/examples/latte/in.latte.water
+lmp_serial -in lammps/examples/latte/in.latte.water
This pair style was written in collaboration with the LATTE
developers.
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index 13a6ad1d629a9d24662bdb232a30bfe0c0c7e635..98e55398728c06caf536ee925b988f359376d84a 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -94,26 +94,26 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal fix neb command");
if (strcmp(arg[iarg+1],"first") == 0) {
FreeEndIni = true;
- kspringIni = force->numeric(FLERR,arg[iarg+2]);
+ kspringIni = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last") == 0) {
FreeEndFinal = true;
FinalAndInterWithRespToEIni = false;
FreeEndFinalWithRespToEIni = false;
- kspringFinal = force->numeric(FLERR,arg[iarg+2]);
+ kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last/efirst") == 0) {
FreeEndFinal = false;
FinalAndInterWithRespToEIni = false;
FreeEndFinalWithRespToEIni = true;
- kspringFinal = force->numeric(FLERR,arg[iarg+2]);
+ kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last/efirst/middle") == 0) {
FreeEndFinal = false;
FinalAndInterWithRespToEIni = true;
FreeEndFinalWithRespToEIni = true;
- kspringFinal = force->numeric(FLERR,arg[iarg+2]);
+ kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else error->all(FLERR,"Illegal fix neb command");
iarg += 3;
-
+
} else error->all(FLERR,"Illegal fix neb command");
}
@@ -298,12 +298,14 @@ void FixNEB::min_post_force(int vflag)
if (ireplica == 0) vIni=veng;
if (FreeEndFinalWithRespToEIni) {
- if (me == 0) {
+ if (cmode == SINGLE_PROC_DIRECT || cmode == SINGLE_PROC_MAP) {
int procFirst;
procFirst=universe->root_proc[0];
MPI_Bcast(&vIni,1,MPI_DOUBLE,procFirst,uworld);
- }
- if (cmode == MULTI_PROC) {
+ }else {
+ if (me == 0)
+ MPI_Bcast(&vIni,1,MPI_DOUBLE,0,rootworld);
+
MPI_Bcast(&vIni,1,MPI_DOUBLE,0,world);
}
}
@@ -313,8 +315,8 @@ void FixNEB::min_post_force(int vflag)
// if (me == 0 )
if (update->ntimestep == 0) {
EIniIni = veng;
- // if (cmode == MULTI_PROC)
- // MPI_Bcast(&EIniIni,1,MPI_DOUBLE,0,world);
+ // if (cmode == MULTI_PROC)
+ // MPI_Bcast(&EIniIni,1,MPI_DOUBLE,0,world);
}
}*/
@@ -360,7 +362,7 @@ void FixNEB::min_post_force(int vflag)
tangent[i][2]=delzp;
tlen += tangent[i][0]*tangent[i][0] +
tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
- dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
+ dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
f[i][2]*tangent[i][2];
}
}
@@ -383,9 +385,9 @@ void FixNEB::min_post_force(int vflag)
tangent[i][0]=delxn;
tangent[i][1]=delyn;
tangent[i][2]=delzn;
- tlen += tangent[i][0]*tangent[i][0] +
+ tlen += tangent[i][0]*tangent[i][0] +
tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
- dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
+ dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
f[i][2]*tangent[i][2];
}
}
@@ -431,15 +433,15 @@ void FixNEB::min_post_force(int vflag)
}
nlen += delxn*delxn + delyn*delyn + delzn*delzn;
- tlen += tangent[i][0]*tangent[i][0] +
+ tlen += tangent[i][0]*tangent[i][0] +
tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
dotpath += delxp*delxn + delyp*delyn + delzp*delzn;
- dottangrad += tangent[i][0]*f[i][0] +
+ dottangrad += tangent[i][0]*f[i][0] +
tangent[i][1]*f[i][1] + tangent[i][2]*f[i][2];
- gradnextlen += fnext[i][0]*fnext[i][0] +
+ gradnextlen += fnext[i][0]*fnext[i][0] +
fnext[i][1]*fnext[i][1] +fnext[i][2] * fnext[i][2];
- dotgrad += f[i][0]*fnext[i][0] + f[i][1]*fnext[i][1] +
+ dotgrad += f[i][0]*fnext[i][0] + f[i][1]*fnext[i][1] +
f[i][2]*fnext[i][2];
springF[i][0] = kspringPerp*(delxn-delxp);
@@ -514,9 +516,10 @@ void FixNEB::min_post_force(int vflag)
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
- if (dot<0) prefactor = -dot - kspringFinal*(veng-EFinalIni);
- else prefactor = -dot + kspringFinal*(veng-EFinalIni);
-
+ if (veng<EFinalIni) {
+ if (dot<0) prefactor = -dot - kspringFinal*(veng-EFinalIni);
+ else prefactor = -dot + kspringFinal*(veng-EFinalIni);
+ }
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] += prefactor *tangent[i][0];
@@ -531,10 +534,10 @@ void FixNEB::min_post_force(int vflag)
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
-
- if (dot<0) prefactor = -dot - kspringFinal*(veng-vIni);
- else prefactor = -dot + kspringFinal*(veng-vIni);
-
+ if (veng<vIni) {
+ if (dot<0) prefactor = -dot - kspringFinal*(veng-vIni);
+ else prefactor = -dot + kspringFinal*(veng-vIni);
+ }
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] += prefactor *tangent[i][0];
@@ -589,7 +592,7 @@ void FixNEB::min_post_force(int vflag)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
+ dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
f[i][2]*tangent[i][2];
dotSpringTangent += springF[i][0]*tangent[i][0] +
springF[i][1]*tangent[i][1] + springF[i][2]*tangent[i][2];}
@@ -625,11 +628,11 @@ void FixNEB::min_post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- f[i][0] += prefactor*tangent[i][0] +
+ f[i][0] += prefactor*tangent[i][0] +
AngularContr*(springF[i][0] - dotSpringTangent*tangent[i][0]);
- f[i][1] += prefactor*tangent[i][1] +
+ f[i][1] += prefactor*tangent[i][1] +
AngularContr*(springF[i][1] - dotSpringTangent*tangent[i][1]);
- f[i][2] += prefactor*tangent[i][2] +
+ f[i][2] += prefactor*tangent[i][2] +
AngularContr*(springF[i][2] - dotSpringTangent*tangent[i][2]);
}
}
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 3e36c8f7a937b0e254389c4099897a62aa9ac236..cac5e0b49c8181802b324a932de23aa7f61d7abb 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -34,6 +34,10 @@
#include <stdio.h>
#include <math.h>
+#ifdef LAMMPS_BIGBIG
+#error "The USER-INTEL package is not compatible with -DLAMMPS_BIGBIG"
+#endif
+
#ifdef _LMP_INTEL_OFFLOAD
#ifndef INTEL_OFFLOAD_NOAFFINITY
#include <unistd.h>
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index ad3c97c9df0e61b0f998e078eb1ea4fa2cfead61..54c5055812ef7b4ecdc1edd41a02af7b257e1e55 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -127,7 +127,7 @@ struct KernelArgsAIREBOT {
struct NeighListAIREBO neigh_rebo;
PairAIREBOIntelParam<flt_t,acc_t> params;
struct AtomAIREBOT<flt_t> * x; /* num_all */
- int * tag; /* num_all */
+ tagint * tag; /* num_all */
flt_t * nC, * nH; /* num_all */
int * map; /* num_types+1 */
struct ResultForceT<acc_t> * result_f; /* num_all */
@@ -399,7 +399,7 @@ void PairAIREBOIntel::eval(
const int * _noalias const numneigh = list->numneigh;
const int * _noalias const cnumneigh = buffers->cnumneigh(list);
const int * _noalias const firstneigh = buffers->firstneigh(list);
- int * const tag = atom->tag;
+ tagint * const tag = atom->tag;
const int ntypes = atom->ntypes + 1;
const int eatom = this->eflag_atom;
@@ -1912,10 +1912,10 @@ template<typename flt_t, typename acc_t>
void ref_torsion(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
- int * tag = ka->tag;
+ tagint * tag = ka->tag;
for (int ii = ka->frebo_from_atom; ii < ka->frebo_to_atom; ii++) {
int i = ii;
- int itag = tag[i];
+ tagint itag = tag[i];
int itype = map[x[i].w];
if (itype != 0) continue;
flt_t xtmp = x[i].x;
@@ -1925,7 +1925,7 @@ void ref_torsion(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
int jnum = ka->neigh_rebo.num[i];
for (int jj = 0; jj < jnum; jj++) {
int j = REBO_neighs_i[jj];
- int jtag = tag[j];
+ tagint jtag = tag[j];
if (itag > jtag) {
if (((itag+jtag) & 1) == 0) continue;
@@ -2039,9 +2039,9 @@ void ref_frebo_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
template<typename flt_t, typename acc_t>
inline void ref_frebo_single_atom(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i) {
AtomAIREBOT<flt_t> * x = ka->x;
- int * tag = ka->tag;
+ tagint * tag = ka->tag;
int jj;
- int itag = tag[i];
+ tagint itag = tag[i];
flt_t x_i = x[i].x;
flt_t y_i = x[i].y;
flt_t z_i = x[i].z;
@@ -2049,7 +2049,7 @@ inline void ref_frebo_single_atom(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i) {
int jnum = ka->neigh_rebo.num[i];
for (jj = 0; jj < jnum; jj++) {
int j = neighs[jj];
- int jtag = tag[j];
+ tagint jtag = tag[j];
if (itag > jtag) {
if (((itag + jtag) & 1) == 0)
continue;
@@ -2165,9 +2165,7 @@ template<typename flt_t, typename acc_t>
void ref_lennard_jones_single_atom(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
int morseflag) {
AtomAIREBOT<flt_t> * x = ka->x;
- int * tag = ka->tag;
int jj;
- int itag = tag[i];
int * neighs = ka->neigh_lmp.entries + ka->neigh_lmp.offset[i];
int jnum = ka->neigh_lmp.num_half[i];
for (jj = 0; jj < jnum; jj++) {
@@ -3640,7 +3638,6 @@ static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int * i_buf, int * j_buf) {
{ // jump-scope for exceed_limits
AtomAIREBOT<flt_t> * x = ka->x;
- int * tag = ka->tag;
int * map = ka->map;
ResultForceT<acc_t> * result_f = ka->result_f;
flt_t rcminij = ka->params.rcmin[itype][jtype];
@@ -3847,13 +3844,13 @@ exceed_limits:
*/
static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
AtomAIREBOT<flt_t> * _noalias x = ka->x;
- int * _noalias tag = ka->tag;
+ tagint * _noalias tag = ka->tag;
int * _noalias map = ka->map;
int i_buf[2][2][fvec::VL];
int j_buf[2][2][fvec::VL];
int n_buf[2][2] = {0};
for (int i = ka->frebo_from_atom; i < ka->frebo_to_atom; i++) {
- int itag = tag[i];
+ tagint itag = tag[i];
int itype = map[x[i].w];
flt_t x_i = x[i].x;
flt_t y_i = x[i].y;
@@ -3862,7 +3859,7 @@ static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
int jnum = ka->neigh_rebo.num[i];
for (int jj = 0; jj < jnum; jj++) {
int j = neighs[jj];
- int jtag = tag[j];
+ tagint jtag = tag[j];
if (itag > jtag) {
if (((itag + jtag) & 1) == 0)
continue;
@@ -4490,7 +4487,6 @@ exceed_limits:
template<int MORSEFLAG>
static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
AtomAIREBOT<flt_t> * x = ka->x;
- int * tag = ka->tag;
int * map = ka->map;
ResultForceT<acc_t> * result_f = ka->result_f;
ivec c_i1 = ivec::set1(1);
@@ -4521,7 +4517,6 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
int num_bo[2][2] = {0};
for (int i = ka->frebo_from_atom; i < ka->frebo_to_atom; i++) {
- ivec itag_bc = ivec::set1(tag[i]);
int itype = map[x[i].w];
fvec x_i = fvec::set1(x[i].x);
fvec y_i = fvec::set1(x[i].y);
diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp
index 1b212732de66a2928cc9c5dbf2d28bb71e12485b..21aed6c7c04665555727e1b89b45ecdf67732a64 100644
--- a/src/USER-OMP/fix_neigh_history_omp.cpp
+++ b/src/USER-OMP/fix_neigh_history_omp.cpp
@@ -98,7 +98,7 @@ void FixNeighHistoryOMP::pre_exchange_onesided()
// nlocal can be larger if other fixes added atoms at this pre_exchange()
// clear per-thread paged data structures
-
+
MyPage <tagint> &ipg = ipage_atom[tid];
MyPage <double> &dpg = dpage_atom[tid];
ipg.reset();
@@ -540,8 +540,8 @@ void FixNeighHistoryOMP::post_neighbor()
int *allflags;
double *allvalues;
- MyPage <tagint> &ipg = ipage_atom[tid];
- MyPage <double> &dpg = dpage_atom[tid];
+ MyPage <int> &ipg = ipage_neigh[tid];
+ MyPage <double> &dpg = dpage_neigh[tid];
ipg.reset();
dpg.reset();
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 2a0d65b6422a3165169e8bb653d94a731012ac7f..d2d72a855a8ff261e58a00a8002c6e5c19e25153 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -1099,7 +1099,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
------------------------------------------------------------------------- */
int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1121,7 +1121,7 @@ void AtomVecSMD::data_vel(int m, char **values) {
------------------------------------------------------------------------- */
int AtomVecSMD::data_vel_hybrid(int m, char **values) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1143,10 +1143,14 @@ void AtomVecSMD::pack_data(double **buf) {
buf[i][7] = x[i][0];
buf[i][8] = x[i][1];
buf[i][9] = x[i][2];
-
- buf[i][10] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
- buf[i][11] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
- buf[i][12] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
+
+ buf[i][10] = x0[i][0];
+ buf[i][11] = x0[i][1];
+ buf[i][12] = x0[i][2];
+
+ buf[i][13] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
+ buf[i][14] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
+ buf[i][15] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
@@ -1155,7 +1159,7 @@ void AtomVecSMD::pack_data(double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1167,9 +1171,9 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
for (int i = 0; i < n; i++)
fprintf(fp,
TAGINT_FORMAT
- " %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", (tagint) ubuf(buf[i][0]).i,
+ " %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i,
(int) ubuf(buf[i][1]).i, (int) ubuf(buf[i][2]).i, buf[i][3], buf[i][4], buf[i][5], buf[i][6], buf[i][7], buf[i][8],
- buf[i][9], (int) ubuf(buf[i][7]).i, (int) ubuf(buf[i][8]).i, (int) ubuf(buf[i][9]).i);
+ buf[i][9], buf[i][10], buf[i][11], buf[i][12]);
}
/* ----------------------------------------------------------------------
@@ -1177,7 +1181,7 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1200,7 +1204,7 @@ void AtomVecSMD::pack_vel(double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1211,8 +1215,7 @@ int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
for (int i = 0; i < n; i++)
fprintf(fp, TAGINT_FORMAT
- " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3],
- buf[i][4], buf[i][5], buf[i][6]);
+ " %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3]);
}
/* ----------------------------------------------------------------------
@@ -1220,7 +1223,7 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 3;
}
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index c62c6df91c5f1ddfbb197aff8b7d12cc7edd215f..ff62e867877205e0e10b10f25e96acc30fbe9b8a 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -306,6 +306,10 @@ void CreateBonds::many()
nadd_bonds,atom->nbonds);
}
}
+ // trigger clearing the list of available neighbor list requests
+ // and a full rebuild of them during the next run setup.
+ // otherwise the request from this command may linger around.
+ neighbor->init();
}
/* ---------------------------------------------------------------------- */
@@ -338,6 +342,7 @@ void CreateBonds::single_bond()
bond_atom[m][num_bond[m]] = batom2;
num_bond[m]++;
}
+ ++atom->nbonds;
if (force->newton_bond) return;
@@ -385,6 +390,7 @@ void CreateBonds::single_angle()
angle_atom3[m][num_angle[m]] = aatom3;
num_angle[m]++;
}
+ ++atom->nangles;
if (force->newton_bond) return;
@@ -448,6 +454,7 @@ void CreateBonds::single_dihedral()
dihedral_atom4[m][num_dihedral[m]] = datom4;
num_dihedral[m]++;
}
+ ++atom->ndihedrals;
if (force->newton_bond) return;
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 489c5bf5d5f4ce5837d42ee64d8fcd04be3103f3..a4219dbecbc271a0c9c136767a970b2a955c6aff 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -407,6 +407,10 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
break;
}
}
+ // trigger clearing the list of available neighbor list requests
+ // and a full rebuild of them during the next run setup.
+ // otherwise the request from this command may linger around.
+ neighbor->init();
}
/* ----------------------------------------------------------------------