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Merge pull request #510 from akohlmey/collected-small-changes

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Collected small changes
This commit is contained in:
sjplimp
2017-06-15 11:12:14 -06:00
committed by GitHub
parent 1a29048940 b62d526cc9
commit d3c90f3c14
81 changed files with 633 additions and 1318 deletions
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doc/src/Eqs/pair_lj_sf.jpg
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11
doc/src/Eqs/pair_lj_sf.tex
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@ -1,11 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
\mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
\end{eqnarray*}
\end{document}

1
doc/src/Section_commands.txt
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@ -1039,7 +1039,6 @@ package"_Section_start.html#start_3.
"lj/sdk (gko)"_pair_sdk.html,
"lj/sdk/coul/long (go)"_pair_sdk.html,
"lj/sdk/coul/msm (o)"_pair_sdk.html,
"lj/sf (o)"_pair_lj_sf.html,
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,

4
doc/src/Section_packages.txt
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@ -2027,8 +2027,8 @@ algorithm to formulate single-particle constraint functions
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
n = grad(g).
[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The
Netherlands)
[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
[Install or un-install:]

2
doc/src/fix_adapt.txt
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@ -47,7 +47,7 @@ keyword = {scale} or {reset} :l
fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size
fix 1 all adapt 10 atom diameter v_size :pre
variable ramp_up equal "ramp(0.01,0.5)"
fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre

6
doc/src/fix_deform.txt
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@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
This fix will restore the initial box settings from "binary restart
files"_restart.html, which allows the fix to be properly continue
deformation, when using the start/stop options of the "run"_run.html
command. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15.

1
doc/src/lammps.book
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@ -447,7 +447,6 @@ pair_lj96.html
pair_lj_cubic.html
pair_lj_expand.html
pair_lj_long.html
pair_lj_sf.html
pair_lj_smooth.html
pair_lj_smooth_linear.html
pair_lj_soft.html

114
doc/src/pair_lj_sf.txt
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@ -1,114 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/sf command :h3
pair_style lj/sf/omp command :h3
[Syntax:]
pair_style lj/sf cutoff :pre
cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
[Examples:]
pair_style lj/sf 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 3.0 :pre
[Description:]
Style {lj/sf} computes a truncated and force-shifted LJ interaction
(Shifted Force Lennard-Jones), so that both the potential and the
force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd:
:c,image(Eqs/pair_lj_sf.jpg)
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma
coefficients and cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The
default mix value is {geometric}. See the "pair_modify" command for
details.
The "pair_modify"_pair_modify.html shift option is not relevant for
this pair style, since the pair interaction goes to 0.0 at the cutoff.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Toxvaerd)
[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).

31
doc/src/pair_lj_smooth_linear.txt
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@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3
[Syntax:]
pair_style lj/smooth/linear Rc :pre
pair_style lj/smooth/linear cutoff :pre
Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
[Examples:]
pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0 :pre
pair_style lj/smooth/linear 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.3 3.0 9.0 :pre
[Description:]
Style {lj/smooth/linear} computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:
Style {lj/smooth/linear} computes a truncated and force-shifted LJ
interaction (aka Shifted Force Lennard-Jones) that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term based
on the cutoff distance, so that both, the potential and the force, go
continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd:
:c,image(Eqs/pair_lj_smooth_linear.jpg)
At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -41,8 +41,8 @@ epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global value
for Rc is used.
The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.
:line
@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
shift option for the energy of the pair interaction, since it goes
to 0.0 at the cutoff by construction.
The "pair_modify"_pair_modify.html table option is not relevant for
this pair style.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and

1
doc/src/pairs.txt
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@ -49,7 +49,6 @@ Pair Styles :h1
pair_lj_cubic
pair_lj_expand
pair_lj_long
pair_lj_sf
pair_lj_smooth
pair_lj_smooth_linear
pair_lj_soft

6
doc/src/set.txt
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@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
value can be an atom-style variable (see below)
{image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
any of nx,ny,nz can be an atom-style variable (see below)
{bond} value = bond type for all bonds between selected atoms
{angle} value = angle type for all angles between selected atoms
{dihedral} value = dihedral type for all dihedrals between selected atoms
@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
"dump"_dump.html command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified. This keyword does not allow use of atom-style variables.
nx,ny,nz, then the current image value for that dimension is unchanged.
For non-periodic dimensions only a value of 0 can be specified.
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they

8
doc/src/special_bonds.txt
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@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these
potentials, though such bonds may exist elsewhere in your system,
e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated.
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a manybody potential will alter the
neigborlist and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
that is not possible - use a special bonds setting of 1.0 1.0 1.0.
NOTE: Unlike some commands in LAMMPS, you cannot use this command
multiple times in an incremental fashion: e.g. to first set the LJ

12
lib/meam/meam_dens_final.F
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@ -98,13 +98,14 @@ c Complete the calculation of density
call G_gam(Gamma(i),ibar_meam(elti),
$ gsmooth_factor,G,errorflag)
if (errorflag.ne.0) return
call get_shpfcn(shp,lattce_meam(elti,elti))
if (ibar_meam(elti).le.0) then
Gbar = 1.d0
dGbar = 0.d0
else
call get_shpfcn(shp,lattce_meam(elti,elti))
if (mix_ref_t.eq.1) then
gam = (t_ave(1,i)*shpi(1)+t_ave(2,i)*shpi(2)
$ +t_ave(3,i)*shpi(3))/(Z*Z)
gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
$ +t_ave(3,i)*shp(3))/(Z*Z)
else
gam = (t1_meam(elti)*shp(1)+t2_meam(elti)*shp(2)
$ +t3_meam(elti)*shp(3))/(Z*Z)
@ -119,9 +120,8 @@ c Complete the calculation of density
Gbar = 1.d0
dGbar = 0.d0
else
call get_shpfcn(shpi,lattce_meam(elti,elti))
gam = (t_ave(1,i)*shpi(1)+t_ave(2,i)*shpi(2)
$ +t_ave(3,i)*shpi(3))/(Z*Z)
gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
$ +t_ave(3,i)*shp(3))/(Z*Z)
call dG_gam(gam,ibar_meam(elti),gsmooth_factor,
$ Gbar,dGbar)
endif

2
src/.gitignore vendored
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@ -740,8 +740,6 @@
/pair_lj_sdk_coul_long.h
/pair_lj_sdk_coul_msm.cpp
/pair_lj_sdk_coul_msm.h
/pair_lj_sf.cpp
/pair_lj_sf.h
/pair_lj_sf_dipole_sf.cpp
/pair_lj_sf_dipole_sf.h
/pair_lubricateU.cpp

10
src/KOKKOS/npair_kokkos.cpp
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@ -287,12 +287,12 @@ int NeighborKokkosExecute<DeviceType>::exclusion(const int &i,const int &j,
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule
if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] == molecule[j]) return 1;
} else // exclude i-j pair if on different molecules
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] != molecule[j]) return 1;
molecule[i] == molecule[j]) return 1;
} else // exclude i-j pair if on different molecules
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] != molecule[j]) return 1;
}
return 0;

2
src/KOKKOS/npair_kokkos.h
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@ -385,7 +385,7 @@ struct NPairKokkosBuildFunctor {
}
#ifdef KOKKOS_HAVE_CUDA
__device__ inline
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
c.template build_ItemCuda<HALF_NEIGH,GHOST_NEWTON,TRI>(dev);
}

26
src/MC/fix_gcmc.cpp
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@ -501,7 +501,7 @@ void FixGCMC::init()
if (ifix < 0) error->all(FLERR,"Fix gcmc rigid fix does not exist");
fixrigid = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
if (&onemols[imol] != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix gcmc and fix rigid/small not using "
"same molecule template ID");
@ -516,7 +516,7 @@ void FixGCMC::init()
if (ifix < 0) error->all(FLERR,"Fix gcmc shake fix does not exist");
fixshake = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
if (&onemols[imol] != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix gcmc and fix shake not using "
"same molecule template ID");
}
@ -1397,12 +1397,13 @@ void FixGCMC::attempt_molecule_insertion()
// FixRigidSmall::set_molecule stores rigid body attributes
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
for (int submol = 0; submol < nmol; ++submol) {
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,submol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,submol,com_coord,vnew,quat);
}
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
@ -2058,11 +2059,12 @@ void FixGCMC::attempt_molecule_insertion_full()
// FixRigidSmall::set_molecule stores rigid body attributes
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
for (int submol = 0; submol < nmol; ++submol) {
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,submol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,submol,com_coord,vnew,quat);
}
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");

5
src/Purge.list
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@ -16,6 +16,11 @@ style_region.h
style_neigh_bin.h
style_neigh_pair.h
style_neigh_stencil.h
# deleted on 6 June 2017
pair_lj_sf.cpp
pair_lj_sf.h
pair_lj_sf_omp.cpp
pair_lj_sf_omp.h
# deleted on 4 May 2017
dump_custom_vtk.cpp
dump_custom_vtk.h

2
src/RIGID/fix_rigid.cpp
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@ -50,7 +50,7 @@ enum{ISO,ANISO,TRICLINIC};
#define EPSILON 1.0e-7
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
#define LINERTIA (1.0/12.0) // moment of inertia prefactor for line segment
/* ---------------------------------------------------------------------- */

4
src/RIGID/fix_rigid_small.cpp
View File

@ -54,7 +54,7 @@ FixRigidSmall *FixRigidSmall::frsptr;
#define BIG 1.0e20
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
#define LINERTIA (1.0/12.0) // moment of inertia prefactor for line segment
#define DELTA_BODY 10000
@ -1047,7 +1047,7 @@ int FixRigidSmall::dof(int tgroup)
j = atom2body[i];
counts[j][2]++;
if (mask[i] & tgroupbit) {
if (extended && eflags[i]) counts[j][1]++;
if (extended && (eflags[i] & ~(POINT | DIPOLE))) counts[j][1]++;
else counts[j][0]++;
}
}

14
src/USER-INTEL/nbin_intel.cpp
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@ -55,7 +55,7 @@ NBinIntel::~NBinIntel() {
nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
}
}
/* ----------------------------------------------------------------------
setup for bin_atoms()
@ -71,7 +71,7 @@ void NBinIntel::bin_atoms_setup(int nall)
if (_offload_alloc) {
const int * binhead = this->binhead;
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead:alloc_if(0) free_if(1))
nocopy(binhead:alloc_if(0) free_if(1))
}
#endif
@ -99,7 +99,7 @@ void NBinIntel::bin_atoms_setup(int nall)
const int * _atombin = this->_atombin;
const int * _binpacked = this->_binpacked;
#pragma offload_transfer target(mic:_cop) \
nocopy(bins,_atombin,_binpacked:alloc_if(0) free_if(1))
nocopy(bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
memory->destroy(bins);
@ -157,10 +157,10 @@ void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
const flt_t dx = (INTEL_BIGP - bboxhi[0]);
const flt_t dy = (INTEL_BIGP - bboxhi[1]);
const flt_t dz = (INTEL_BIGP - bboxhi[2]);
if (dx * dx + dy * dy + dz * dz <
static_cast<flt_t>(neighbor->cutneighmaxsq))
if (dx * dx + dy * dy + dz * dz <
static_cast<flt_t>(neighbor->cutneighmaxsq))
error->one(FLERR,
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
}
// ---------- Grow and cast/pack buffers -------------
@ -181,7 +181,7 @@ void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
_fix->stop_watch(TIME_PACK);

222
src/USER-INTEL/npair_full_bin_intel.cpp
View File

@ -70,12 +70,12 @@ fbi(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
#endif
buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end,
_fix->nbor_pack_width());
_fix->nbor_pack_width());
int need_ic = 0;
if (atom->molecular)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);
neighbor->cutneighmax);
#ifdef _LMP_INTEL_OFFLOAD
if (need_ic) {
@ -167,7 +167,7 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
overflow = _fix->get_off_overflow_flag();
_fix->stop_watch(TIME_HOST_NEIGHBOR);
_fix->start_watch(TIME_OFFLOAD_LATENCY);
} else
} else
#endif
{
tnum = comm->nthreads;
@ -255,8 +255,8 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
ito += astart;
int e_ito = ito;
if (ito == num) {
int imod = ito % pack_width;
if (imod) e_ito += pack_width - imod;
int imod = ito % pack_width;
if (imod) e_ito += pack_width - imod;
}
const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
int which;
@ -276,91 +276,91 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
const int ioffset = ntypes * itype;
const int ibin = atombin[i];
int raw_count = pack_offset;
int raw_count = pack_offset;
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
if (exclude) {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
if (exclude) {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
int j = binpacked[jj];
#endif
for (int jj = bstart; jj < bend; jj++) {
int j = binpacked[jj];
if (i == j) j=e_nall;
if (i == j) j=e_nall;
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
#endif
#endif
#ifndef _LMP_INTEL_OFFLOAD
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
neighptr[raw_count++] = j;
neighptr[raw_count++] = j;
}
}
} else {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
} else {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
int j = binpacked[jj];
for (int jj = bstart; jj < bend; jj++) {
int j = binpacked[jj];
if (i == j) j=e_nall;
if (i == j) j=e_nall;
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
#endif
#endif
neighptr[raw_count++] = j;
neighptr[raw_count++] = j;
}
}
}
}
if (raw_count > obound) *overflow = 1;
if (raw_count > obound) *overflow = 1;
#if defined(LMP_SIMD_COMPILER)
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
#endif
#else
#pragma vector aligned
#endif
#else
#pragma vector aligned
#pragma simd
#endif
#endif
for (int u = pack_offset; u < raw_count; u++) {
#endif
#endif
for (int u = pack_offset; u < raw_count; u++) {
int j = neighptr[u];
const flt_t delx = xtmp - x[j].x;
const flt_t dely = ytmp - x[j].y;
const flt_t delz = ztmp - x[j].z;
const int jtype = x[j].w;
const flt_t rsq = delx * delx + dely * dely + delz * delz;
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (need_ic) {
int no_special;
ominimum_image_check(no_special, delx, dely, delz);
@ -376,73 +376,73 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
if (j > vgmax) vgmax = j;
}
#endif
}
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
lmin = MIN(lmin,vlmin);
gmin = MIN(gmin,vgmin);
lmax = MAX(lmax,vlmax);
gmax = MAX(gmax,vgmax);
lmin = MIN(lmin,vlmin);
gmin = MIN(gmin,vgmin);
lmax = MAX(lmax,vlmax);
gmax = MAX(gmax,vgmax);
#endif
int n = lane, n2 = pack_offset;
for (int u = pack_offset; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
const int jtag = tag[pj];
int flist = 0;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) flist = 1;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) flist = 1;
} else {
for (int u = pack_offset; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
const int jtag = tag[pj];
int flist = 0;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) flist = 1;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) flist = 1;
} else {
if (x[pj].z < ztmp) flist = 1;
else if (x[pj].z == ztmp && x[pj].y < ytmp) flist = 1;
else if (x[pj].z == ztmp && x[pj].y == ytmp && x[pj].x < xtmp)
flist = 1;
}
if (flist) {
neighptr[n2++] = j;
} else {
neighptr[n] = j;
n += pack_width;
}
else if (x[pj].z == ztmp && x[pj].y < ytmp) flist = 1;
else if (x[pj].z == ztmp && x[pj].y == ytmp && x[pj].x < xtmp)
flist = 1;
}
if (flist) {
neighptr[n2++] = j;
} else {
neighptr[n] = j;
n += pack_width;
}
}
}
int ns = (n - lane) / pack_width;
atombin[i] = ns;
for (int u = pack_offset; u < n2; u++) {
neighptr[n] = neighptr[u];
n += pack_width;
}
int ns = (n - lane) / pack_width;
atombin[i] = ns;
for (int u = pack_offset; u < n2; u++) {
neighptr[n] = neighptr[u];
n += pack_width;
}
ilist[i] = i;
cnumneigh[i] = ct + lane;
ns += n2 - pack_offset;
ns += n2 - pack_offset;
numneigh[i] = ns;
if (ns > max_chunk) max_chunk = ns;
lane++;
if (lane == pack_width) {
ct += max_chunk * pack_width;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
const int edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
max_chunk = 0;
pack_offset = maxnbors * pack_width;
lane = 0;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
if (ns > max_chunk) max_chunk = ns;
lane++;
if (lane == pack_width) {
ct += max_chunk * pack_width;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
const int edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
max_chunk = 0;
pack_offset = maxnbors * pack_width;
lane = 0;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
}
}
}
if (*overflow == 1)
@ -482,13 +482,13 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
const int trip = jnum * pack_width;
const int trip = jnum * pack_width;
for (int jj = 0; jj < trip; jj+=pack_width) {
const int j = jlist[jj];
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
ofind_special(which, special, nspecial, i, tag[j]);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
@ -511,9 +511,9 @@ fbi(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
int jj = 0;
for (jj = 0; jj < jnum; jj++) {
if (jlist[jj] >= nlocal) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
}
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
}
}
}
}

4
src/USER-INTEL/npair_full_bin_intel.h
View File

@ -15,7 +15,7 @@
NPairStyle(full/bin/intel,
NPairFullBinIntel,
NP_FULL | NP_BIN | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI |
NP_FULL | NP_BIN | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI |
NP_INTEL)
#else
@ -38,7 +38,7 @@ class NPairFullBinIntel : public NPairIntel {
void fbi(NeighList *, IntelBuffers<flt_t,acc_t> *);
template <class flt_t, class acc_t, int, int>
void fbi(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
const int, const int offload_end = 0);
const int, const int offload_end = 0);
};
}

80
src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
View File

@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtoffIntel::NPairHalfBinNewtoffIntel(LAMMPS *lmp) :
NPairHalfBinNewtoffIntel::NPairHalfBinNewtoffIntel(LAMMPS *lmp) :
NPairIntel(lmp) {}
/* ----------------------------------------------------------------------
@ -75,7 +75,7 @@ hbnni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
int need_ic = 0;
if (atom->molecular)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);
neighbor->cutneighmax);
#ifdef _LMP_INTEL_OFFLOAD
if (need_ic) {
@ -159,7 +159,7 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
overflow = _fix->get_off_overflow_flag();
_fix->stop_watch(TIME_HOST_NEIGHBOR);
_fix->start_watch(TIME_OFFLOAD_LATENCY);
} else
} else
#endif
{
tnum = comm->nthreads;
@ -294,13 +294,13 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[n++] = -j - 1;
else
else
neighptr[n++] = j;
} else
neighptr[n++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
#endif
} else {
if (need_ic) {
@ -308,16 +308,16 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[n2++] = -j - 1;
else
else
neighptr[n2++] = j;
} else
neighptr[n2++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#endif
}
}
}
}
}
}
ilist[i] = i;
@ -341,13 +341,13 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
neighptr += n;
if (ct + n + maxnbors > list_size) {
*overflow = 1;
ct = (ifrom + tid) * maxnbors;
ct = (ifrom + tid) * maxnbors;
}
}
if (*overflow == 1)
for (int i = ifrom; i < ito; i++)
numneigh[i] = 0;
for (int i = ifrom; i < ito; i++)
numneigh[i] = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
@ -370,7 +370,7 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
@ -383,38 +383,38 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj];
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
ofind_special(which, special, nspecial, i, tag[j]);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
if (j >= nlocal) {
if (j == nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
if (which) jlist[jj] = j ^ (which << SBBITS);
if (which) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
@ -438,9 +438,9 @@ hbnni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
_fix->start_watch(TIME_PACK);
_fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(_fix->host_min_local(),
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->stop_watch(TIME_PACK);
}
}

2
src/USER-INTEL/npair_half_bin_newtoff_intel.h
View File

@ -38,7 +38,7 @@ class NPairHalfBinNewtoffIntel : public NPairIntel {
void hbnni(NeighList *, IntelBuffers<flt_t,acc_t> *);
template <class flt_t, class acc_t, int>
void hbnni(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
const int);
const int);
};
}

356
src/USER-INTEL/npair_half_bin_newton_intel.cpp
View File

@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) :
NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) :
NPairIntel(lmp) {}
/* ----------------------------------------------------------------------
@ -75,7 +75,7 @@ hbni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
int need_ic = 0;
if (atom->molecular)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);
neighbor->cutneighmax);
#ifdef _LMP_INTEL_OFFLOAD
if (need_ic) {
@ -96,7 +96,7 @@ hbni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
}
}
#else
if (need_ic)
if (need_ic)
hbni<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
else
hbni<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
@ -119,7 +119,7 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
if (offload) {
if (INTEL_MIC_NBOR_PAD > 1)
pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
} else
} else
#endif
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
@ -172,7 +172,7 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
overflow = _fix->get_off_overflow_flag();
_fix->stop_watch(TIME_HOST_NEIGHBOR);
_fix->start_watch(TIME_OFFLOAD_LATENCY);
} else
} else
#endif
{
tnum = comm->nthreads;
@ -235,8 +235,8 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
int end = stencil[k] + 1;
for (int kk = k + 1; kk < nstencil; kk++) {
if (stencil[kk-1]+1 == stencil[kk]) {
end++;
k++;
end++;
k++;
} else break;
}
binend[nstencilp] = end;
@ -262,8 +262,8 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
ito += astart;
int e_ito = ito;
if (ito == num) {
int imod = ito % swidth;
if (imod) e_ito += swidth - imod;
int imod = ito % swidth;
if (imod) e_ito += swidth - imod;
}
const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
#else
@ -294,118 +294,118 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above/to the right" of i
int raw_count = pack_offset;
int raw_count = pack_offset;
for (int j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
#ifdef _LMP_INTEL_OFFLOAD
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost && offload) continue;
#endif
#endif
if (x[j].z < ztmp) continue;
if (x[j].z == ztmp) {
if (x[j].y < ytmp) continue;
if (x[j].y == ytmp && x[j].x < xtmp) continue;
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (offload_noghost && i < offload_end) continue;
#endif
#endif
#ifndef _LMP_INTEL_OFFLOAD
if (exclude) {
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
}
#endif
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
}
#endif
neighptr[raw_count++] = j;
}
neighptr[raw_count++] = j;
}
// loop over all atoms in other bins in stencil, store every pair
const int ibin = atombin[i];
if (exclude) {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
const int j = binpacked[jj];
if (exclude) {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
const int j = binpacked[jj];
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
#endif
#endif
#ifndef _LMP_INTEL_OFFLOAD
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
neighptr[raw_count++] = j;
}
}
} else {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
const int j = binpacked[jj];
neighptr[raw_count++] = j;
}
}
} else {
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
#ifndef _LMP_INTEL_OFFLOAD
#ifdef INTEL_VMASK
#pragma simd
#endif
#endif
for (int jj = bstart; jj < bend; jj++) {
const int j = binpacked[jj];
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
#endif
#endif
neighptr[raw_count++] = j;
}
}
}
neighptr[raw_count++] = j;
}
}
}
if (raw_count > obound) *overflow = 1;
if (raw_count > obound) *overflow = 1;
#if defined(LMP_SIMD_COMPILER)
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
#endif
#else
#pragma vector aligned
#endif
#else
#pragma vector aligned
#pragma simd
#endif
#endif
for (int u = pack_offset; u < raw_count; u++) {
#endif
#endif
for (int u = pack_offset; u < raw_count; u++) {
int j = neighptr[u];
const flt_t delx = xtmp - x[j].x;
const flt_t dely = ytmp - x[j].y;
const flt_t delz = ztmp - x[j].z;
const int jtype = x[j].w;
const int jtype = x[j].w;
const flt_t rsq = delx * delx + dely * dely + delz * delz;
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (need_ic) {
int no_special;
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[u] = -j - 1;
}
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (need_ic) {
int no_special;
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[u] = -j - 1;
}
#ifdef _LMP_INTEL_OFFLOAD
if (j < nlocal) {
if (j < vlmin) vlmin = j;
@ -415,40 +415,40 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
if (j > vgmax) vgmax = j;
}
#endif
}
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
lmin = MIN(lmin,vlmin);
gmin = MIN(gmin,vgmin);
lmax = MAX(lmax,vlmax);
gmax = MAX(gmax,vgmax);
lmin = MIN(lmin,vlmin);
gmin = MIN(gmin,vgmin);
lmax = MAX(lmax,vlmax);
gmax = MAX(gmax,vgmax);
#endif
int n = lane, n2 = pack_offset;
for (int u = pack_offset; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
for (int u = pack_offset; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
if (pj < nlocal) {
neighptr[n] = j;
n += swidth;
} else
neighptr[n2++] = j;
}
}
int ns = (n - lane) / swidth;
for (int u = pack_offset; u < n2; u++) {
neighptr[n] = neighptr[u];
n += swidth;
}
if (pj < nlocal) {
neighptr[n] = j;
n += swidth;
} else
neighptr[n2++] = j;
}
}
int ns = (n - lane) / swidth;
for (int u = pack_offset; u < n2; u++) {
neighptr[n] = neighptr[u];
n += swidth;
}
ilist[i] = i;
cnumneigh[i] = ct + lane;
ns += n2 - pack_offset;
#ifndef OUTER_CHUNK
ns += n2 - pack_offset;
#ifndef OUTER_CHUNK
int edge = (ns % pad_width);
if (edge) {
const int pad_end = ns + (pad_width - edge);
@ -458,41 +458,41 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
for ( ; ns < pad_end; ns++)
neighptr[ns] = e_nall;
}
#endif
#endif
numneigh[i] = ns;
#ifdef OUTER_CHUNK
if (ns > max_chunk) max_chunk = ns;
lane++;
if (lane == swidth) {
ct += max_chunk * swidth;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
int edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
max_chunk = 0;
pack_offset = maxnbors * swidth;
lane = 0;
if (ct + obound > list_size) {
#ifdef OUTER_CHUNK
if (ns > max_chunk) max_chunk = ns;
lane++;
if (lane == swidth) {
ct += max_chunk * swidth;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
int edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
max_chunk = 0;
pack_offset = maxnbors * swidth;
lane = 0;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
}
#else
ct += ns;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
#endif
}
}
#else
ct += ns;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
#endif
}
if (*overflow == 1)
@ -505,25 +505,25 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
#pragma omp critical
#endif
{
if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
}
#pragma omp barrier
#pragma omp barrier
}
int ghost_offset = 0, nall_offset = e_nall;
if (separate_buffers) {
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
}
#endif
@ -531,49 +531,49 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
#ifndef OUTER_CHUNK
#ifndef OUTER_CHUNK
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma vector aligned
#pragma simd
#endif
#endif
for (int jj = 0; jj < jnum; jj++) {
#else
const int trip = jnum * swidth;
#else
const int trip = jnum * swidth;
for (int jj = 0; jj < trip; jj+= swidth) {
#endif
#endif
const int j = jlist[jj];
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
ofind_special(which, special, nspecial, i, tag[j]);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
#endif
if (which) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
@ -597,9 +597,9 @@ hbni(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
_fix->start_watch(TIME_PACK);
_fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(_fix->host_min_local(),
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->stop_watch(TIME_PACK);
}
}

4
src/USER-INTEL/npair_half_bin_newton_intel.h
View File

@ -37,8 +37,8 @@ class NPairHalfBinNewtonIntel : public NPairIntel {
template <class flt_t, class acc_t>
void hbni(NeighList *, IntelBuffers<flt_t,acc_t> *);
template <class flt_t, class acc_t, int, int>
void hbni(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
const int, const int offload_end = 0);
void hbni(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
const int, const int offload_end = 0);
};
}

178
src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
View File

@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) :
NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) :
NPairIntel(lmp) {}
/* ----------------------------------------------------------------------
@ -75,7 +75,7 @@ hbnti(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
int need_ic = 0;
if (atom->molecular)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);
neighbor->cutneighmax);
#ifdef _LMP_INTEL_OFFLOAD
if (need_ic) {
@ -171,7 +171,7 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
overflow = _fix->get_off_overflow_flag();
_fix->stop_watch(TIME_HOST_NEIGHBOR);
_fix->start_watch(TIME_OFFLOAD_LATENCY);
} else
} else
#endif
{
tnum = comm->nthreads;
@ -279,20 +279,20 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
const int ibin = atombin[i];
int raw_count = maxnbors;
int raw_count = maxnbors;
for (int k = 0; k < nstencilp; k++) {
const int bstart = binhead[ibin + binstart[k]];
const int bend = binhead[ibin + binend[k]];
for (int jj = bstart; jj < bend; jj++) {
const int j = binpacked[jj];
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
#endif
#endif
if (x[j].z < ztmp) continue;
if (x[j].z == ztmp) {
@ -305,45 +305,45 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
#ifndef _LMP_INTEL_OFFLOAD
if (exclude) {
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
}
#endif
const int jtype = x[j].w;
if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
}
#endif
neighptr[raw_count++] = j;
}
}
if (raw_count > obound)
*overflow = 1;
neighptr[raw_count++] = j;
}
}
if (raw_count > obound)
*overflow = 1;
#if defined(LMP_SIMD_COMPILER)
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#ifdef _LMP_INTEL_OFFLOAD
int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
#endif
#else
#pragma vector aligned
#endif
#else
#pragma vector aligned
#pragma simd
#endif
#endif
for (int u = maxnbors; u < raw_count; u++) {
#endif
#endif
for (int u = maxnbors; u < raw_count; u++) {
int j = neighptr[u];
const flt_t delx = xtmp - x[j].x;
const flt_t dely = ytmp - x[j].y;
const flt_t delz = ztmp - x[j].z;
const int jtype = x[j].w;
const int jtype = x[j].w;
const flt_t rsq = delx * delx + dely * dely + delz * delz;
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (rsq > cutneighsq[ioffset + jtype])
neighptr[u] = e_nall;
else {
if (need_ic) {
int no_special;
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[u] = -j - 1;
}
int no_special;
ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
neighptr[u] = -j - 1;
}
#ifdef _LMP_INTEL_OFFLOAD
if (j < nlocal) {
@ -358,26 +358,26 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
}
int n = 0, n2 = maxnbors;
for (int u = maxnbors; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
for (int u = maxnbors; u < raw_count; u++) {
const int j = neighptr[u];
int pj = j;
if (pj < e_nall) {
if (need_ic)
if (pj < 0) pj = -pj - 1;
if (pj < nlocal)
neighptr[n++] = j;
else
neighptr[n2++] = j;
}
}
int ns = n;
for (int u = maxnbors; u < n2; u++)
neighptr[n++] = neighptr[u];
if (pj < nlocal)
neighptr[n++] = j;
else
neighptr[n2++] = j;
}
}
int ns = n;
for (int u = maxnbors; u < n2; u++)
neighptr[n++] = neighptr[u];
ilist[i] = i;
cnumneigh[i] = ct;
ns += n2 - maxnbors;
ns += n2 - maxnbors;
int edge = (ns % pad_width);
if (edge) {
@ -390,17 +390,17 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
}
numneigh[i] = ns;
ct += ns;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
ct += ns;
const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
edge = (ct % alignb);
if (edge) ct += alignb - edge;
neighptr = firstneigh + ct;
if (ct + obound > list_size) {
if (i < ito - 1) {
*overflow = 1;
ct = (ifrom + tid * 2) * maxnbors;
}
}
}
if (*overflow == 1)
@ -428,7 +428,7 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
@ -440,43 +440,43 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma vector aligned
#pragma simd
#endif
#endif
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj];
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
if (need_ic && j < 0) {
which = 0;
jlist[jj] = -j - 1;
} else
ofind_special(which, special, nspecial, i, tag[j]);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
if (which) jlist[jj] = j ^ (which << SBBITS);
if (which) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
@ -500,9 +500,9 @@ hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
_fix->start_watch(TIME_PACK);
_fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(_fix->host_min_local(),
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->host_used_local(),
_fix->host_min_ghost(),
_fix->host_used_ghost());
_fix->stop_watch(TIME_PACK);
}
}

2
src/USER-INTEL/npair_half_bin_newton_tri_intel.h
View File

@ -38,7 +38,7 @@ class NPairHalfBinNewtonTriIntel : public NPairIntel {
void hbnti(NeighList *, IntelBuffers<flt_t,acc_t> *);
template <class flt_t, class acc_t, int, int>
void hbnti(const int, NeighList *, IntelBuffers<flt_t,acc_t> *, const int,
const int, const int offload_end = 0);
const int, const int offload_end = 0);
};
}

2
src/USER-INTEL/npair_intel.cpp
View File

@ -62,6 +62,6 @@ void NPairIntel::grow_stencil()
const int maxstencil = ns->get_maxstencil();
#pragma offload_transfer target(mic:_cop) \
in(stencil:length(maxstencil) alloc_if(1) free_if(0))
}
}
}
#endif

8
src/USER-MANIFOLD/README
View File

@ -7,10 +7,14 @@ box). It achieves this using the RATTLE constraint algorithm applied
to single-particle constraint functions g(xi,yi,zi) = 0 and their
derivative (i.e. the normal of the manifold) n = grad(g).
Stefan Paquay, s.paquay@tue.nl
Applied Physics/Theory of Polymers and Soft Matter,
Stefan Paquay, stefanpaquay@gmail.com
until 2017: Applied Physics/Theory of Polymers and Soft Matter,
Eindhoven University of Technology (TU/e), The Netherlands
since 2017: Brandeis University, Waltham, MA, USA.
Thanks to Remy Kusters at TU/e for testing.
This software is distributed under the GNU General Public License.

1
src/USER-MISC/README
View File

@ -64,7 +64,6 @@ pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12

10
src/USER-MISC/pair_cdeam.cpp
View File

@ -456,11 +456,11 @@ void PairCDEAM::read_h_coeff(char *filename)
{
if(comm->me == 0) {
// Open potential file
FILE *fp;
FILE *fptr;
char line[MAXLINE];
char nextline[MAXLINE];
fp = force->open_potential(filename);
if (fp == NULL) {
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s", filename);
error->one(FLERR,str);
@ -468,7 +468,7 @@ void PairCDEAM::read_h_coeff(char *filename)
// h coefficients are stored at the end of the file.
// Skip to last line of file.
while(fgets(nextline, MAXLINE, fp) != NULL) {
while(fgets(nextline, MAXLINE, fptr) != NULL) {
strcpy(line, nextline);
}
char* ptr = strtok(line, " \t\n\r\f");
@ -483,7 +483,7 @@ void PairCDEAM::read_h_coeff(char *filename)
error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
// Close the potential file.
fclose(fp);
fclose(fptr);
}
MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);

355
src/USER-MISC/pair_lj_sf.cpp
View File

@ -1,355 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Laurent Joly (U Lyon), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_lj_sf.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJShiftedForce::PairLJShiftedForce(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairLJShiftedForce::~PairLJShiftedForce()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(foffset);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJShiftedForce::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
t = r/cut[itype][jtype];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
t*foffset[itype][jtype];
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
(t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJShiftedForce::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(foffset,n+1,n+1,"pair:foffset");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJShiftedForce::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
if (cut_global <= 0.0)
error->all(FLERR,"Illegal pair_style command");
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJShiftedForce::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
if (cut_one <= 0.0)
error->all(FLERR,"Incorrect args for pair coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJShiftedForce::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
double ratio = sigma[i][j] / cut[i][j];
foffset[i][j] = 4.0 * epsilon[i][j] * (12.0 * pow(ratio,12.0) -
6.0 * pow(ratio,6.0));
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
cut[j][i] = cut[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
foffset[j][i] = foffset[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJShiftedForce::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJShiftedForce::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJShiftedForce::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJShiftedForce::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairLJShiftedForce::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
t = r/cut[itype][jtype];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
t*foffset[itype][jtype];
fforce = factor_lj*forcelj*r2inv;
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
(t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
return factor_lj*philj;
}

53
src/USER-MISC/pair_lj_sf.h
View File

@ -1,53 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/sf,PairLJShiftedForce)
#else
#ifndef LMP_PAIR_LJ_SF_H
#define LMP_PAIR_LJ_SF_H
#include "pair.h"
namespace LAMMPS_NS {
class PairLJShiftedForce : public Pair {
public:
PairLJShiftedForce(class LAMMPS *);
virtual ~PairLJShiftedForce();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
protected:
double cut_global;
double **cut;
double **epsilon,**sigma;
double **lj1,**lj2,**lj3,**lj4,**foffset,**offset;
void allocate();
};
}
#endif
#endif

2
src/USER-OMP/fix_rigid_omp.cpp
View File

@ -39,7 +39,7 @@ using namespace MathConst;
enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
typedef struct { double x,y,z; } dbl3_t;

2
src/USER-OMP/fix_rigid_small_omp.cpp
View File

@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};

164
src/USER-OMP/pair_lj_sf_omp.cpp
View File

@ -1,164 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_lj_sf_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJShiftedForceOMP::PairLJShiftedForceOMP(LAMMPS *lmp) :
PairLJShiftedForce(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairLJShiftedForceOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double t,rsq,r2inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
t = sqrt(rsq)/cut[itype][jtype];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
t*foffset[itype][jtype];
fpair = factor_lj*forcelj*r2inv;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
(t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
evdwl *= factor_lj;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}
/* ---------------------------------------------------------------------- */
double PairLJShiftedForceOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairLJShiftedForce::memory_usage();
return bytes;
}

48
src/USER-OMP/pair_lj_sf_omp.h
View File

@ -1,48 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/sf/omp,PairLJShiftedForceOMP)
#else
#ifndef LMP_PAIR_LJ_SF_OMP_H
#define LMP_PAIR_LJ_SF_OMP_H
#include "pair_lj_sf.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
class PairLJShiftedForceOMP : public PairLJShiftedForce, public ThrOMP {
public:
PairLJShiftedForceOMP(class LAMMPS *);
virtual void compute(int, int);
virtual double memory_usage();
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void eval(int ifrom, int ito, ThrData * const thr);
};
}
#endif
#endif

1
src/USER-OMP/pair_lj_smooth_linear_omp.h
View File

@ -18,6 +18,7 @@
#ifdef PAIR_CLASS
PairStyle(lj/smooth/linear/omp,PairLJSmoothLinearOMP)
PairStyle(lj/sf/omp,PairLJSmoothLinearOMP)
#else

2
src/compute.h
View File

@ -153,7 +153,7 @@ class Compute : protected Pointers {
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
inline int sbmask(int j) {
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}

33
src/compute_orientorder_atom.cpp
View File

@ -102,23 +102,22 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
if (qlist[iw] > qmax) qmax = qlist[iw];
}
iarg += nqlist;
if (strcmp(arg[iarg],"components") == 0) {
qlcompflag = 1;
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");
qlcomp = force->numeric(FLERR,arg[iarg+1]);
if (qlcomp <= 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
iqlcomp = -1;
for (int iw = 0; iw < nqlist; iw++)
if (qlcomp == qlist[iw]) {
iqlcomp = iw;
break;
}
if (iqlcomp < 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
iarg += 2;
}
} else if (strcmp(arg[iarg],"components") == 0) {
qlcompflag = 1;
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");
qlcomp = force->numeric(FLERR,arg[iarg+1]);
if (qlcomp <= 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
iqlcomp = -1;
for (int iw = 0; iw < nqlist; iw++)
if (qlcomp == qlist[iw]) {
iqlcomp = iw;
break;
}
if (iqlcomp < 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");

2
src/create_bonds.h
View File

@ -30,7 +30,7 @@ class CreateBonds : protected Pointers {
void command(int, char **);
private:
inline int sbmask(int j) {
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}
};

2
src/delete_atoms.h
View File

@ -45,7 +45,7 @@ class DeleteAtoms : protected Pointers {
void recount_topology();
void options(int, char **);
inline int sbmask(int j) {
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}

2
src/domain.cpp
View File

@ -60,6 +60,7 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
{
box_exist = 0;
box_change = 0;
dimension = 3;
nonperiodic = 0;
@ -1697,6 +1698,7 @@ int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed)
void Domain::set_lattice(int narg, char **arg)
{
if (lattice) delete lattice;
lattice = NULL;
lattice = new Lattice(lmp,narg,arg);
}

55
src/fix_deform.cpp
View File

@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{NONE,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
// same as domain.cpp, fix_nvt_sllod.cpp, compute_temp_deform.cpp
@ -52,6 +52,7 @@ rfix(NULL), irregular(NULL), set(NULL)
if (narg < 4) error->all(FLERR,"Illegal fix deform command");
no_change_box = 1;
restart_global = 1;
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix deform command");
@ -59,12 +60,7 @@ rfix(NULL), irregular(NULL), set(NULL)
// set defaults
set = new Set[6];
set[0].style = set[1].style = set[2].style =
set[3].style = set[4].style = set[5].style = NONE;
set[0].hstr = set[1].hstr = set[2].hstr =
set[3].hstr = set[4].hstr = set[5].hstr = NULL;
set[0].hratestr = set[1].hratestr = set[2].hratestr =
set[3].hratestr = set[4].hratestr = set[5].hratestr = NULL;
memset(set,0,6*sizeof(Set));
// parse arguments
@ -343,11 +339,9 @@ rfix(NULL), irregular(NULL), set(NULL)
set[i].hi_initial = domain->boxhi[i];
set[i].vol_initial = domain->xprd * domain->yprd * domain->zprd;
}
for (int i = 3; i < 6; i++) {
if (i == 5) set[i].tilt_initial = domain->xy;
else if (i == 4) set[i].tilt_initial = domain->xz;
else if (i == 3) set[i].tilt_initial = domain->yz;
}
set[3].tilt_initial = domain->yz;
set[4].tilt_initial = domain->xz;
set[5].tilt_initial = domain->xy;
// reneighboring only forced if flips can occur due to shape changes
@ -955,6 +949,43 @@ void FixDeform::end_of_step()
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
write Set data to restart file
------------------------------------------------------------------------- */
void FixDeform::write_restart(FILE *fp)
{
if (comm->me == 0) {
int size = 6*sizeof(Set);
fwrite(&size,sizeof(int),1,fp);
fwrite(set,sizeof(Set),6,fp);
}
}
/* ----------------------------------------------------------------------
use selected state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixDeform::restart(char *buf)
{
int samestyle = 1;
Set *set_restart = (Set *) buf;
for (int i=0; i<6; ++i) {
// restore data from initial state
set[i].lo_initial = set_restart[i].lo_initial;
set[i].hi_initial = set_restart[i].hi_initial;
set[i].vol_initial = set_restart[i].vol_initial;
set[i].tilt_initial = set_restart[i].tilt_initial;
// check if style settings are consitent (should do the whole set?)
if (set[i].style != set_restart[i].style)
samestyle = 0;
if (set[i].substyle != set_restart[i].substyle)
samestyle = 0;
}
if (!samestyle)
error->all(FLERR,"Fix deform settings not consistent with restart");
}
/* ---------------------------------------------------------------------- */
void FixDeform::options(int narg, char **arg)

2
src/fix_deform.h
View File

@ -35,6 +35,8 @@ class FixDeform : public Fix {
void init();
virtual void pre_exchange();
virtual void end_of_step();
virtual void write_restart(FILE *);
virtual void restart(char *buf);
double memory_usage();
protected:

2
src/fix_lineforce.cpp
View File

@ -29,6 +29,8 @@ using namespace FixConst;
FixLineForce::FixLineForce(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
dynamic_group_allow = 1;
if (narg != 6) error->all(FLERR,"Illegal fix lineforce command");
xdir = force->numeric(FLERR,arg[3]);
ydir = force->numeric(FLERR,arg[4]);

2
src/fix_planeforce.cpp
View File

@ -29,6 +29,8 @@ using namespace FixConst;
FixPlaneForce::FixPlaneForce(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
dynamic_group_allow = 1;
if (narg != 6) error->all(FLERR,"Illegal fix planeforce command");
xdir = force->numeric(FLERR,arg[3]);
ydir = force->numeric(FLERR,arg[4]);

12
src/npair.cpp
View File

@ -123,7 +123,7 @@ void NPair::copy_bin_info()
mbinxlo = nb->mbinxlo;
mbinylo = nb->mbinylo;
mbinzlo = nb->mbinzlo;
bininvx = nb->bininvx;
bininvy = nb->bininvy;
bininvz = nb->bininvz;
@ -183,15 +183,15 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
// intra-chain: exclude i-j pair if in same molecule
// inter-chain: exclude i-j pair if in different molecules
// intra-chain: exclude i-j pair if in same molecule
// inter-chain: exclude i-j pair if in different molecules
if (ex_mol_intra[m]) {
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] == molecule[j]) return 1;
molecule[i] == molecule[j]) return 1;
} else {
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] != molecule[j]) return 1;
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] != molecule[j]) return 1;
}
}

2
src/npair.h
View File

@ -79,7 +79,7 @@ class NPair : protected Pointers {
double bininvx,bininvy,bininvz;
int *atom2bin,*bins;
int *binhead;
// data from NStencil class
int nstencil;

2
src/npair_full_bin.h
View File

@ -15,7 +15,7 @@
NPairStyle(full/bin,
NPairFullBin,
NP_FULL | NP_BIN | NP_MOLONLY |
NP_FULL | NP_BIN | NP_MOLONLY |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

2
src/npair_full_bin_atomonly.h
View File

@ -16,7 +16,7 @@
NPairStyle(full/bin/atomonly,
NPairFullBinAtomonly,
NP_FULL | NP_BIN | NP_ATOMONLY |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

2
src/npair_full_bin_ghost.h
View File

@ -15,7 +15,7 @@
NPairStyle(full/bin/ghost,
NPairFullBinGhost,
NP_FULL | NP_BIN | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
NP_FULL | NP_BIN | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
NP_ORTHO | NP_TRI)
#else

2
src/npair_full_nsq_ghost.h
View File

@ -15,7 +15,7 @@
NPairStyle(full/nsq/ghost,
NPairFullNsqGhost,
NP_FULL | NP_NSQ | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
NP_FULL | NP_NSQ | NP_GHOST | NP_NEWTON | NP_NEWTOFF |
NP_ORTHO | NP_TRI)
#else

2
src/npair_half_bin_atomonly_newton.cpp
View File

@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfBinAtomonlyNewton::NPairHalfBinAtomonlyNewton(LAMMPS *lmp) :
NPairHalfBinAtomonlyNewton::NPairHalfBinAtomonlyNewton(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------

2
src/npair_half_respa_bin_newton_tri.cpp
View File

@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfRespaBinNewtonTri::NPairHalfRespaBinNewtonTri(LAMMPS *lmp) :
NPairHalfRespaBinNewtonTri::NPairHalfRespaBinNewtonTri(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------

2
src/npair_half_size_bin_newton.cpp
View File

@ -190,7 +190,7 @@ void NPairHalfSizeBinNewton::build(NeighList *list)
nn += dnum;
}
}
n++;
}
}

2
src/npair_half_size_bin_newton_tri.cpp
View File

@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeBinNewtonTri::NPairHalfSizeBinNewtonTri(LAMMPS *lmp) :
NPairHalfSizeBinNewtonTri::NPairHalfSizeBinNewtonTri(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------

4
src/npair_skip_respa.h
View File

@ -15,8 +15,8 @@
NPairStyle(skip/half/respa,
NPairSkipRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI |
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

2
src/npair_skip_size.cpp
View File

@ -32,7 +32,7 @@ NPairSkipSize::NPairSkipSize(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
if list requests it, preserve shear history via fix shear/history
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void NPairSkipSize::build(NeighList *list)

2
src/npair_skip_size.h
View File

@ -15,7 +15,7 @@
NPairStyle(skip/half/size,
NPairSkipSize,
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

2
src/npair_skip_size_off2on.cpp
View File

@ -33,7 +33,7 @@ NPairSkipSizeOff2on::NPairSkipSizeOff2on(LAMMPS *lmp) : NPair(lmp) {}
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
parent non-skip list used newton off, this skip list is newton on
if list requests it, preserve shear history via fix shear/history
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void NPairSkipSizeOff2on::build(NeighList *list)

4
src/npair_skip_size_off2on.h
View File

@ -15,8 +15,8 @@
NPairStyle(skip/size/off2on,
NPairSkipSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI |
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else

4
src/npair_skip_size_off2on_oneside.cpp
View File

@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------
@ -35,7 +35,7 @@ NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
iskip and ijskip flag which atom types and type pairs to skip
parent non-skip list used newton off and was not onesided,
this skip list is newton on and onesided
if list requests it, preserve shear history via fix shear/history
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void NPairSkipSizeOff2onOneside::build(NeighList *list)

4
src/npair_skip_size_off2on_oneside.h
View File

@ -15,8 +15,8 @@
NPairStyle(skip/size/off2on/oneside,
NPairSkipSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF |
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF |
NP_ORTHO | NP_TRI)
#else

2
src/nstencil_full_bin_2d.cpp
View File

@ -28,7 +28,7 @@ NStencilFullBin2d::NStencilFullBin2d(LAMMPS *lmp) : NStencil(lmp) {}
void NStencilFullBin2d::create()
{
int i,j;
nstencil = 0;
for (j = -sy; j <= sy; j++)

2
src/nstencil_full_bin_2d.h
View File

@ -15,7 +15,7 @@
NStencilStyle(full/bin/2d,
NStencilFullBin2d,
NS_FULL | NS_BIN | NS_2D |
NS_FULL | NS_BIN | NS_2D |
NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/nstencil_full_bin_3d.h
View File

@ -15,7 +15,7 @@
NStencilStyle(full/bin/3d,
NStencilFullBin3d,
NS_FULL | NS_BIN | NS_3D |
NS_FULL | NS_BIN | NS_3D |
NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/nstencil_full_ghost_bin_2d.h
View File

@ -15,7 +15,7 @@
NStencilStyle(full/ghost/bin/2d,
NStencilFullGhostBin2d,
NS_FULL | NS_GHOST | NS_BIN | NS_2D |
NS_FULL | NS_GHOST | NS_BIN | NS_2D |
NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/nstencil_full_ghost_bin_3d.h
View File

@ -15,7 +15,7 @@
NStencilStyle(full/ghost/bin/3d,
NStencilFullGhostBin3d,
NS_FULL | NS_GHOST | NS_BIN | NS_3D |
NS_FULL | NS_GHOST | NS_BIN | NS_3D |
NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/nstencil_full_multi_2d.h
View File

@ -15,7 +15,7 @@
NStencilStyle(full/multi/2d,
NStencilFullMulti2d,
NS_FULL | NS_MULTI | NS_2D |
NS_FULL | NS_MULTI | NS_2D |
NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/nstencil_half_bin_2d_newtoff.cpp
View File

@ -19,7 +19,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) :
NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------

2
src/nstencil_half_bin_2d_newton_tri.cpp
View File

@ -19,7 +19,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) :
NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------

2
src/nstencil_half_bin_3d_newtoff.cpp
View File

@ -19,7 +19,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) :
NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------

2
src/nstencil_half_bin_3d_newton_tri.cpp
View File

@ -19,7 +19,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) :
NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------

2
src/nstencil_half_ghost_bin_2d_newtoff.h
View File

@ -15,7 +15,7 @@
NStencilStyle(half/ghost/bin/2d/newtoff,
NStencilHalfGhostBin2dNewtoff,
NS_HALF | NS_GHOST | NS_BIN | NS_2D |
NS_HALF | NS_GHOST | NS_BIN | NS_2D |
NS_NEWTOFF | NS_ORTHO | NS_TRI)
#else

2
src/pair.h
View File

@ -245,7 +245,7 @@ class Pair : protected Pointers {
ubuf(int arg) : i(arg) {}
};
inline int sbmask(int j) {
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}
};

1
src/pair_lj_smooth_linear.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS
PairStyle(lj/smooth/linear,PairLJSmoothLinear)
PairStyle(lj/sf,PairLJSmoothLinear)
#else

12
src/set.cpp
View File

@ -327,15 +327,18 @@ void Set::command(int narg, char **arg)
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
ximage = force->inumeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else ximage = force->inumeric(FLERR,arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
yimage = force->inumeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yimage = force->inumeric(FLERR,arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
zimage = force->inumeric(FLERR,arg[iarg+3]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zimage = force->inumeric(FLERR,arg[iarg+3]);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all(FLERR,
@ -811,6 +814,9 @@ void Set::set(int keyword)
int xbox = (atom->image[i] & IMGMASK) - IMGMAX;
int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX;
if (varflag1) ximage = static_cast<int>(xvalue);
if (varflag2) yimage = static_cast<int>(yvalue);
if (varflag3) zimage = static_cast<int>(zvalue);
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;

4
src/write_restart.cpp
View File

@ -185,7 +185,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart fileper "
error->all(FLERR,"Cannot use write_restart fileper "
"without % in restart file name");
int nper = force->inumeric(FLERR,arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal write_restart command");
@ -203,7 +203,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart nfile "
error->all(FLERR,"Cannot use write_restart nfile "
"without % in restart file name");
int nfile = force->inumeric(FLERR,arg[iarg+1]);
if (nfile <= 0) error->all(FLERR,"Illegal write_restart command");