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20 changed files with 122 additions and 88 deletions

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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="16 Dec 2016 version">
<META NAME="docnumber" CONTENT="21 Dec 2016 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
16 Dec 2016 version :c,h4
21 Dec 2016 version :c,h4
Version info: :h4

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@ -43,7 +43,7 @@ ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) :
size_peratom_cols = 4;
nmax = 0;
if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)");
}

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@ -34,7 +34,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixEOStableRX::FixEOStableRX(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), ntables(0), tables(NULL),
Fix(lmp, narg, arg), ntables(0), tables(NULL),
tables2(NULL), dHf(NULL), eosSpecies(NULL)
{
if (narg != 8) error->all(FLERR,"Illegal fix eos/table/rx command");

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@ -60,12 +60,12 @@ double getElapsedTime( const TimerType &t0, const TimerType &t1) { return t1-t0;
/* ---------------------------------------------------------------------- */
FixRX::FixRX(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
kineticsFile(NULL), id_fix_species(NULL),
Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
kineticsFile(NULL), id_fix_species(NULL),
id_fix_species_old(NULL), fix_species(NULL), fix_species_old(NULL)
{
if (narg < 7 || narg > 12) error->all(FLERR,"Illegal fix rx command");
@ -656,7 +656,7 @@ void FixRX::setup_pre_force(int vflag)
memset(dpdThetaLocal, 0, sizeof(double)*count);
computeLocalTemperature();
}
for (int id = 0; id < nlocal; id++)
for (int ispecies=0; ispecies<nspecies; ispecies++){
tmp = atom->dvector[ispecies][id];
@ -667,14 +667,14 @@ void FixRX::setup_pre_force(int vflag)
// Set the reaction rate constants to zero: no reactions occur at step 0
for(int irxn=0;irxn<nreactions;irxn++)
kR[irxn] = 0.0;
kR[irxn] = 0.0;
if (odeIntegrationFlag == ODE_LAMMPS_RK4)
rk4(i,NULL);
rk4(i,NULL);
else if (odeIntegrationFlag == ODE_LAMMPS_RKF45)
rkf45(i,NULL);
rkf45(i,NULL);
}
// Communicate the updated momenta and velocities to all nodes
comm->forward_comm_fix(this);
if(localTempFlag) delete [] dpdThetaLocal;

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -147,7 +147,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil_half; k++) {
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
j = bins_ssa[j]) {
jtype = type[j];
@ -183,7 +183,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) {
for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
j = bins_ssa[j]) {
jtype = type[j];

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */

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@ -15,7 +15,7 @@
NPairStyle(halffull/newton/ssa,
NPairHalffullNewtonSSA,
NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
NP_ORTHO | NP_TRI | NP_SSA)
#else

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
NStencilSSA(lmp) {}
/* ----------------------------------------------------------------------

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
NStencilSSA(lmp) {}
/* ----------------------------------------------------------------------
@ -62,7 +62,7 @@ void NStencilHalfBin3dNewtonSSA::create()
// For k==0, make sure to skip already included bins
k = 0;
k = 0;
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;

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@ -182,7 +182,7 @@ void PairDPDfdt::compute(int eflag, int vflag)
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
randnum = random->gaussian();
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
/ (2.0*force->boltz*temperature);
// conservative force = a0 * wd

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@ -206,7 +206,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
wd = wr*wr;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
@ -214,11 +214,11 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
dot = delx*delvx + dely*delvy + delz*delvz;
randnum = random->gaussian();
// Compute the current temperature
theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
theta_ij = 1.0/theta_ij;
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
// Compute the current temperature
theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
theta_ij = 1.0/theta_ij;
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
/ (2.0*force->boltz*theta_ij);
// conservative force = a0 * wr
@ -239,44 +239,44 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
}
if (rmass) {
mass_i = rmass[i];
mass_j = rmass[j];
} else {
mass_i = mass[itype];
mass_j = mass[jtype];
}
massinv_i = 1.0 / mass_i;
massinv_j = 1.0 / mass_j;
if (rmass) {
mass_i = rmass[i];
mass_j = rmass[j];
} else {
mass_i = mass[itype];
mass_j = mass[jtype];
}
massinv_i = 1.0 / mass_i;
massinv_j = 1.0 / mass_j;
// Compute the mechanical and conductive energy, uMech and uCond
mu_ij = massinv_i + massinv_j;
mu_ij *= force->ftm2v;
// Compute the mechanical and conductive energy, uMech and uCond
mu_ij = massinv_i + massinv_j;
mu_ij *= force->ftm2v;
uTmp = gamma_ij*wd*rinv*rinv*dot*dot
uTmp = gamma_ij*wd*rinv*rinv*dot*dot
- 0.5*sigma[itype][jtype]*sigma[itype][jtype]*mu_ij*wd;
uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
uTmp *= 0.5;
uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
uTmp *= 0.5;
duMech[i] += uTmp;
if (newton_pair || j < nlocal) {
duMech[j] += uTmp;
}
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
randPair = alpha_ij*wr*randnum*dtinvsqrt;
duMech[i] += uTmp;
if (newton_pair || j < nlocal) {
duMech[j] += uTmp;
}
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
randPair = alpha_ij*wr*randnum*dtinvsqrt;
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
uTmp += randPair;
duCond[i] += uTmp;
if (newton_pair || j < nlocal) {
duCond[j] -= uTmp;
}
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
uTmp += randPair;
duCond[i] += uTmp;
if (newton_pair || j < nlocal) {
duCond[j] -= uTmp;
}
if (eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);

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@ -182,7 +182,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,0.0,fpair,delx,dely,delz);
0.0,0.0,fpair,delx,dely,delz);
}
}
@ -201,7 +201,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
evdwl *=(pi*cutsq[itype][itype]*cutsq[itype][itype])/84.0;
if (evflag) ev_tally(0,0,nlocal,newton_pair,
evdwl,0.0,0.0,0.0,0.0,0.0);
evdwl,0.0,0.0,0.0,0.0,0.0);
}
if (vflag_fdotr) virial_fdotr_compute();

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@ -847,6 +847,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@ -897,6 +898,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@ -946,6 +948,7 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@ -1050,6 +1053,7 @@ int AtomVecBody::unpack_exchange(double *buf)
inertia[2] = buf[m++];
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in copy()
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,

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@ -57,10 +57,10 @@ namespace LAMMPS_NS {
template<class T>
class MyPage {
public:
int ndatum; // total # of stored datums
int nchunk; // total # of stored chunks
public:
MyPage() {
ndatum = nchunk = 0;
pages = NULL;

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@ -33,7 +33,7 @@ methods:
minchunk <= N <= maxchunk required
put(index) = return indexed chunk to pool (same index returned by get)
int size() = return total size of allocated pages in bytes
public varaibles:
public variables:
ndatum = total # of stored datums
nchunk = total # of stored chunks
size = total size of all allocated pages in daums

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@ -192,6 +192,7 @@ void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
gran calls grow() in granhistory
respaouter calls grow() in respainner, respamiddle
triggered by neighbor list build
not called if a copy list
------------------------------------------------------------------------- */
void NeighList::grow(int nlocal, int nall)

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@ -1369,6 +1369,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
"with ghost neighbors");
// flags for settings the request + system requires of NPair class
// some are set to 0/1, others are set to mask bit
// comparisons below in loop over classes reflect that
// copyflag = no/yes copy request
// skipflag = no/yes skip request
// halfflag = half request (gran and respa are also half lists)
@ -1402,7 +1404,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
// NOTE: exactly one of these request flags is set (see neigh_request.h)
// this requires gran/respaouter also set halfflag
// can simplify this logic, if follow NOTE in neigh_request.h
// all why do size/off2on and size/off2on/oneside set NP_HALF
// why do size/off2on and size/off2on/oneside set NP_HALF
// either should set both half & full, or half should be in file name
// to be consistent with how other NP classes use "half"
@ -1433,9 +1435,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
else if (rq->newton == 1) newtflag = 1;
else if (rq->newton == 2) newtflag = 0;
// use flags to match exactly one of NPair class masks, bit by bit
// copyflag match returns with no further checks
// exactly one of halfflag,fullflag,halffullflag is set and thus must match
// use flags to match exactly one of NPair class masks
// sequence of checks is bit by bit in NeighConst
int mask;
@ -1447,13 +1448,21 @@ int Neighbor::choose_pair(NeighRequest *rq)
for (int i = 0; i < npclass; i++) {
mask = pairmasks[i];
if (copyflag && (mask & NP_COPY)) {
// if copyflag set, return or continue with no further checks
if (copyflag) {
if (!(mask & NP_COPY)) continue;
if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
return i+1;
}
// skipflag must match along with other flags, so do not return
if (skipflag != (mask & NP_SKIP)) continue;
// exactly one of halfflag,fullflag,halffullflag is set and must match
if (halfflag) {
if (!(mask & NP_HALF)) continue;
} else if (fullflag) {
@ -1470,19 +1479,38 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (ssaflag != (mask & NP_SSA)) continue;
if (ompflag != (mask & NP_OMP)) continue;
if (intelflag != (mask & NP_INTEL)) continue;
// style is one of NSQ,BIN,MULTI and must match
if (style == NSQ) {
if (!(mask & NP_NSQ)) continue;
} else if (style == BIN) {
if (!(mask & NP_BIN)) continue;
} else if (style == MULTI) {
if (!(mask & NP_MULTI)) continue;
}
// newtflag is on or off and must match
if (newtflag) {
if (!(mask & NP_NEWTON)) continue;
} else if (!newtflag) {
if (!(mask & NP_NEWTOFF)) continue;
}
// triclinic flag is on or off and must match
if (triclinic) {
if (!(mask & NP_TRI)) continue;
} else if (!triclinic) {
if (!(mask & NP_ORTHO)) continue;
}
// Kokkos flags
if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
if (style == NSQ && !(mask & NP_NSQ)) continue;
if (style == BIN && !(mask & NP_BIN)) continue;
if (style == MULTI && !(mask & NP_MULTI)) continue;
if (newtflag && !(mask & NP_NEWTON)) continue;
if (!newtflag && !(mask & NP_NEWTOFF)) continue;
if (!triclinic && !(mask & NP_ORTHO)) continue;
if (triclinic && !(mask & NP_TRI)) continue;
return i+1;
}
@ -1727,7 +1755,7 @@ void Neighbor::build(int topoflag)
for (i = 0; i < npair_perpetual; i++) {
m = plist[i];
lists[m]->grow(nlocal,nall);
if (!lists[m]->copy) lists[m]->grow(nlocal,nall);
neigh_pair[m]->build_setup();
neigh_pair[m]->build(lists[m]);
}

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@ -15,7 +15,8 @@
NPairStyle(skip,
NPairSkip,
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
NP_SKIP | NP_HALF | NP_FULL | NP_HALFFULL |
NP_NSQ | NP_BIN | NP_MULTI |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

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@ -38,7 +38,7 @@ class Python {
void invoke_function(int, char *) {}
int find(char *) {return -1;}
int variable_match(char *, char *, int) {return -1;}
char *long_string(int) {return NULL;}
};
}

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@ -1 +1 @@
#define LAMMPS_VERSION "16 Dec 2016"
#define LAMMPS_VERSION "21 Dec 2016"