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Merge branch 'master' of https://github.com/lammps/lammps into kk_pair_fix_comm

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This commit is contained in:
Stan Moore
2020-12-22 09:19:18 -07:00
parent 60dc9f6187 8678e82a82
commit ecc98cc05f
66 changed files with 1645 additions and 699 deletions
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8
doc/src/Build_extras.rst
View File

@ -352,7 +352,7 @@ KIM Extra unit tests (CMake only)
During development, testing, or debugging, if
:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
Enabling the extra unit tests have some requirements,
@ -367,9 +367,9 @@ Enabling the extra unit tests have some requirements,
*conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
* It is also necessary to install
``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-build binary of the OpenKIM Repository of
Models or see

6
doc/src/comm_modify.rst
View File

@ -84,13 +84,15 @@ information is available, then also a heuristic based on that bond length
is computed. It is used as communication cutoff, if there is no pair
style present and no *comm_modify cutoff* command used. Otherwise a
warning is printed, if this bond based estimate is larger than the
communication cutoff used. A
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since in this case the communication
cutoffs are determined per atom type, a type specifier is needed and
cutoff for one or multiple types can be extended. Also ranges of types
using the usual asterisk notation can be given.
using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:

18
doc/src/fix_temp_csvr.rst
View File

@ -124,16 +124,16 @@ temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
An important feature of these thermostats is that they have an
An important feature of these thermostats is that they have an
associated effective energy that is a constant of motion.
The effective energy is the total energy (kinetic + potential) plus
the accumulated kinetic energy changes due to the thermostat. The
latter quantity is the global scalar computed by these fixes. This
feature is useful to check the integration of the equations of motion
against discretization errors. In other words, the conservation of
the effective energy can be used to choose an appropriate integration
:doc:`timestep <timestep>`. This is similar to the usual paradigm of
checking the conservation of the total energy in the microcanonical
The effective energy is the total energy (kinetic + potential) plus
the accumulated kinetic energy changes due to the thermostat. The
latter quantity is the global scalar computed by these fixes. This
feature is useful to check the integration of the equations of motion
against discretization errors. In other words, the conservation of
the effective energy can be used to choose an appropriate integration
:doc:`timestep <timestep>`. This is similar to the usual paradigm of
checking the conservation of the total energy in the microcanonical
ensemble.

10
doc/src/neighbor.rst
View File

@ -49,7 +49,9 @@ sometimes be faster. Either style should give the same answers.
The *multi* style is a modified binning algorithm that is useful for
systems with a wide range of cutoff distances, e.g. due to different
size particles. For the *bin* style, the bin size is set to 1/2 of
size particles. For granular pair styles, cutoffs are set to the
sum of the maximum atomic radii for each atom type.
For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
@ -57,8 +59,10 @@ other type pairs have a much shorter cutoff. For style *multi* the
bin size is set to 1/2 of the shortest cutoff distance and multiple
sets of bins are defined to search over for different atom types.
This imposes some extra setup overhead, but the searches themselves
may be much faster for the short-cutoff cases. See the :doc:`comm_modify mode multi <comm_modify>` command for a communication option
that may also be beneficial for simulations of this kind.
may be much faster for the short-cutoff cases.
See the :doc:`comm_modify mode multi <comm_modify>` command for a
communication option that may also be beneficial for simulations of
this kind.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are

2
python/lammps/core.py
View File

@ -77,7 +77,7 @@ class lammps(object):
modpath = dirname(abspath(getsourcefile(lambda:0)))
# for windows installers the shared library is in a different folder
winpath = abspath(os.path.join(modpath,'..','bin'))
winpath = abspath(os.path.join(modpath,'..','..','bin'))
self.lib = None
self.lmp = None

5
src/GPU/pair_lj_cubic_gpu.cpp
View File

@ -16,10 +16,11 @@
------------------------------------------------------------------------- */
#include "pair_lj_cubic_gpu.h"
#include <cmath>
#include <cstdio>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@ -36,6 +37,8 @@
#include "gpu_extra.h"
#include "suffix.h"
#include "pair_lj_cubic_const.h"
using namespace LAMMPS_NS;
using namespace PairLJCubicConstants;

2
src/KIM/pair_kim.cpp
View File

@ -941,7 +941,7 @@ void PairKIM::set_argument_pointers()
// Set KIM pointer appropriately for particleVirial
if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
KIM_SUPPORT_STATUS_required)
KIM_SUPPORT_STATUS_required)
&& (vflag_atom == 0)) {
// reallocate per-atom virial array if necessary
if (atom->nmax > maxvatom) {

2
src/KOKKOS/compute_orientorder_atom_kokkos.cpp
View File

@ -21,6 +21,7 @@
#include "atom_masks.h"
#include "kokkos.h"
#include "math_const.h"
#include "math_special.h"
#include "memory_kokkos.h"
#include "neigh_list.h"
#include "neigh_request.h"
@ -32,6 +33,7 @@
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
using namespace std;
#ifdef DBL_EPSILON

2
src/KOKKOS/pair_zbl_kokkos.cpp
View File

@ -30,6 +30,8 @@
#include "atom_masks.h"
#include "kokkos.h"
#include "pair_zbl_const.h"
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.

2
src/MANYBODY/pair_comb.h
View File

@ -38,7 +38,7 @@ class PairComb : public Pair {
virtual double yasu_char(double *, int &);
double enegtot;
static const int NPARAMS_PER_LINE = 49;
static constexpr int NPARAMS_PER_LINE = 49;
protected:
struct Param {

2
src/MANYBODY/pair_comb3.h
View File

@ -37,7 +37,7 @@ class PairComb3 : public Pair {
virtual double combqeq(double *, int &);
double enegtot;
static const int NPARAMS_PER_LINE = 74;
static constexpr int NPARAMS_PER_LINE = 74;
protected:
// general potential parameters

2
src/MANYBODY/pair_gw.h
View File

@ -34,7 +34,7 @@ class PairGW : public Pair {
void init_style();
double init_one(int, int);
static const int NPARAMS_PER_LINE = 17;
static constexpr int NPARAMS_PER_LINE = 17;
protected:
struct Param {

2
src/MANYBODY/pair_gw_zbl.h
View File

@ -29,7 +29,7 @@ class PairGWZBL : public PairGW {
PairGWZBL(class LAMMPS *);
~PairGWZBL() {}
static const int NPARAMS_PER_LINE = 21;
static constexpr int NPARAMS_PER_LINE = 21;
private:
double global_a_0; // Bohr radius for Coulomb repulsion

2
src/MANYBODY/pair_nb3b_harmonic.h
View File

@ -34,7 +34,7 @@ class PairNb3bHarmonic : public Pair {
double init_one(int, int);
void init_style();
static const int NPARAMS_PER_LINE = 6;
static constexpr int NPARAMS_PER_LINE = 6;
protected:
struct Param {

2
src/MANYBODY/pair_sw.h
View File

@ -34,7 +34,7 @@ class PairSW : public Pair {
virtual double init_one(int, int);
virtual void init_style();
static const int NPARAMS_PER_LINE = 14;
static constexpr int NPARAMS_PER_LINE = 14;
struct Param {
double epsilon,sigma;

2
src/MANYBODY/pair_tersoff.h
View File

@ -34,7 +34,7 @@ class PairTersoff : public Pair {
virtual void init_style();
double init_one(int, int);
static const int NPARAMS_PER_LINE = 17;
static constexpr int NPARAMS_PER_LINE = 17;
protected:

2
src/MANYBODY/pair_tersoff_mod.h
View File

@ -30,7 +30,7 @@ class PairTersoffMOD : public PairTersoff {
PairTersoffMOD(class LAMMPS *);
~PairTersoffMOD() {}
static const int NPARAMS_PER_LINE = 20;
static constexpr int NPARAMS_PER_LINE = 20;
protected:
virtual void read_file(char *);

2
src/MANYBODY/pair_tersoff_mod_c.h
View File

@ -29,7 +29,7 @@ class PairTersoffMODC : public PairTersoffMOD {
PairTersoffMODC(class LAMMPS *lmp) : PairTersoffMOD(lmp) {};
~PairTersoffMODC() {}
static const int NPARAMS_PER_LINE = 21;
static constexpr int NPARAMS_PER_LINE = 21;
protected:
void read_file(char *);

2
src/MANYBODY/pair_tersoff_zbl.h
View File

@ -29,7 +29,7 @@ class PairTersoffZBL : public PairTersoff {
PairTersoffZBL(class LAMMPS *);
~PairTersoffZBL() {}
static const int NPARAMS_PER_LINE = 21;
static constexpr int NPARAMS_PER_LINE = 21;
protected:
double global_a_0; // Bohr radius for Coulomb repulsion

2
src/MANYBODY/pair_vashishta.h
View File

@ -34,7 +34,7 @@ class PairVashishta : public Pair {
double init_one(int, int);
void init_style();
static const int NPARAMS_PER_LINE = 17;
static constexpr int NPARAMS_PER_LINE = 17;
struct Param {
double bigb,gamma,r0,bigc,costheta;

20
src/RIGID/rigid_const.h
View File

@ -33,21 +33,21 @@ namespace LAMMPS_NS {
TORQUE = 1<<8
};
static const double TOLERANCE = 1.0e-6;
static const double EPSILON = 1.0e-7;
static const double BIG = 1.0e20;
static constexpr double TOLERANCE = 1.0e-6;
static constexpr double EPSILON = 1.0e-7;
static constexpr double BIG = 1.0e20;
// moment of inertia prefactor for sphere
static const double SINERTIA = 0.4;
static constexpr double SINERTIA = 0.4;
// moment of inertia prefactor for ellipsoid
static const double EINERTIA = 0.2;
static constexpr double EINERTIA = 0.2;
// moment of inertia prefactor for line segment
static const double LINERTIA = 1.0/12.0;
static constexpr double LINERTIA = 1.0/12.0;
static const int MAXLINE = 1024;
static const int CHUNK = 1024;
static const int DELTA_BODY = 10000;
static const int ATTRIBUTE_PERBODY = 20;
static constexpr int MAXLINE = 1024;
static constexpr int CHUNK = 1024;
static constexpr int DELTA_BODY = 10000;
static constexpr int ATTRIBUTE_PERBODY = 20;
}
}

192
src/SNAP/sna.cpp
View File

@ -18,6 +18,7 @@
#include "sna.h"
#include <cmath>
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
@ -25,6 +26,7 @@
using namespace std;
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
/* ----------------------------------------------------------------------
@ -1363,196 +1365,6 @@ void SNA::destroy_twojmax_arrays()
}
/* ----------------------------------------------------------------------
factorial n, wrapper for precomputed table
------------------------------------------------------------------------- */
double SNA::factorial(int n)
{
if (n < 0 || n > nmaxfactorial) {
char str[128];
sprintf(str, "Invalid argument to factorial %d", n);
error->all(FLERR, str);
}
return nfac_table[n];
}
/* ----------------------------------------------------------------------
factorial n table, size SNA::nmaxfactorial+1
------------------------------------------------------------------------- */
const double SNA::nfac_table[] = {
1,
1,
2,
6,
24,
120,
720,
5040,
40320,
362880,
3628800,
39916800,
479001600,
6227020800,
87178291200,
1307674368000,
20922789888000,
355687428096000,
6.402373705728e+15,
1.21645100408832e+17,
2.43290200817664e+18,
5.10909421717094e+19,
1.12400072777761e+21,
2.5852016738885e+22,
6.20448401733239e+23,
1.5511210043331e+25,
4.03291461126606e+26,
1.08888694504184e+28,
3.04888344611714e+29,
8.8417619937397e+30,
2.65252859812191e+32,
8.22283865417792e+33,
2.63130836933694e+35,
8.68331761881189e+36,
2.95232799039604e+38,
1.03331479663861e+40,
3.71993326789901e+41,
1.37637530912263e+43,
5.23022617466601e+44,
2.03978820811974e+46,
8.15915283247898e+47,
3.34525266131638e+49,
1.40500611775288e+51,
6.04152630633738e+52,
2.65827157478845e+54,
1.1962222086548e+56,
5.50262215981209e+57,
2.58623241511168e+59,
1.24139155925361e+61,
6.08281864034268e+62,
3.04140932017134e+64,
1.55111875328738e+66,
8.06581751709439e+67,
4.27488328406003e+69,
2.30843697339241e+71,
1.26964033536583e+73,
7.10998587804863e+74,
4.05269195048772e+76,
2.35056133128288e+78,
1.3868311854569e+80,
8.32098711274139e+81,
5.07580213877225e+83,
3.14699732603879e+85,
1.98260831540444e+87,
1.26886932185884e+89,
8.24765059208247e+90,
5.44344939077443e+92,
3.64711109181887e+94,
2.48003554243683e+96,
1.71122452428141e+98,
1.19785716699699e+100,
8.50478588567862e+101,
6.12344583768861e+103,
4.47011546151268e+105,
3.30788544151939e+107,
2.48091408113954e+109,
1.88549470166605e+111,
1.45183092028286e+113,
1.13242811782063e+115,
8.94618213078297e+116,
7.15694570462638e+118,
5.79712602074737e+120,
4.75364333701284e+122,
3.94552396972066e+124,
3.31424013456535e+126,
2.81710411438055e+128,
2.42270953836727e+130,
2.10775729837953e+132,
1.85482642257398e+134,
1.65079551609085e+136,
1.48571596448176e+138,
1.3520015276784e+140,
1.24384140546413e+142,
1.15677250708164e+144,
1.08736615665674e+146,
1.03299784882391e+148,
9.91677934870949e+149,
9.61927596824821e+151,
9.42689044888324e+153,
9.33262154439441e+155,
9.33262154439441e+157,
9.42594775983835e+159,
9.61446671503512e+161,
9.90290071648618e+163,
1.02990167451456e+166,
1.08139675824029e+168,
1.14628056373471e+170,
1.22652020319614e+172,
1.32464181945183e+174,
1.44385958320249e+176,
1.58824554152274e+178,
1.76295255109024e+180,
1.97450685722107e+182,
2.23119274865981e+184,
2.54355973347219e+186,
2.92509369349301e+188,
3.3931086844519e+190,
3.96993716080872e+192,
4.68452584975429e+194,
5.5745857612076e+196,
6.68950291344912e+198,
8.09429852527344e+200,
9.8750442008336e+202,
1.21463043670253e+205,
1.50614174151114e+207,
1.88267717688893e+209,
2.37217324288005e+211,
3.01266001845766e+213,
3.8562048236258e+215,
4.97450422247729e+217,
6.46685548922047e+219,
8.47158069087882e+221,
1.118248651196e+224,
1.48727070609069e+226,
1.99294274616152e+228,
2.69047270731805e+230,
3.65904288195255e+232,
5.01288874827499e+234,
6.91778647261949e+236,
9.61572319694109e+238,
1.34620124757175e+241,
1.89814375907617e+243,
2.69536413788816e+245,
3.85437071718007e+247,
5.5502938327393e+249,
8.04792605747199e+251,
1.17499720439091e+254,
1.72724589045464e+256,
2.55632391787286e+258,
3.80892263763057e+260,
5.71338395644585e+262,
8.62720977423323e+264,
1.31133588568345e+267,
2.00634390509568e+269,
3.08976961384735e+271,
4.78914290146339e+273,
7.47106292628289e+275,
1.17295687942641e+278,
1.85327186949373e+280,
2.94670227249504e+282,
4.71472363599206e+284,
7.59070505394721e+286,
1.22969421873945e+289,
2.0044015765453e+291,
3.28721858553429e+293,
5.42391066613159e+295,
9.00369170577843e+297,
1.503616514865e+300, // nmaxfactorial = 167
};
/* ----------------------------------------------------------------------
the function delta given by VMK Eq. 8.2(1)
------------------------------------------------------------------------- */

4
src/SNAP/sna.h
View File

@ -100,10 +100,6 @@ private:
double** dulist_r, ** dulist_i;
int elem_duarray; // element of j in derivative
static const int nmaxfactorial = 167;
static const double nfac_table[];
double factorial(int);
void create_twojmax_arrays();
void destroy_twojmax_arrays();
void init_clebsch_gordan();

2
src/USER-MISC/dihedral_quadratic.cpp
View File

@ -195,6 +195,8 @@ void DihedralQuadratic::compute(int eflag, int vflag)
siinv = 1.0/si;
double dphi = phi-phi0[type];
if (dphi > MY_PI) dphi -= 2*MY_PI;
else if (dphi < -MY_PI) dphi += 2*MY_PI;
p = k[type]*dphi;
pd = - 2.0 * p * siinv;
p = p * dphi;

2
src/USER-MISC/pair_edip.cpp
View File

@ -46,7 +46,7 @@ using namespace LAMMPS_NS;
// max number of interaction per atom for f(Z) environment potential
#define leadDimInteractionList 64
static constexpr int leadDimInteractionList = 64;
/* ---------------------------------------------------------------------- */

5
src/USER-MISC/pair_edip_multi.cpp
View File

@ -32,13 +32,11 @@
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
static const char cite_pair_edip[] =
"@article{cjiang2012\n"
" author = {Jian, Chao and Morgan, Dane, and Szlufarska, Izabella},\n"
@ -56,7 +54,9 @@ static const char cite_pair_edip[] =
" year = {2010},\n"
"}\n\n";
// max number of interaction per atom for f(Z) environment potential
static constexpr int leadDimInteractionList = 64;
/* ---------------------------------------------------------------------- */
@ -94,7 +94,6 @@ PairEDIPMulti::~PairEDIPMulti()
memory->destroy(cutsq);
delete [] map;
//XXX deallocateGrids();
deallocatePreLoops();
}
}

26
src/USER-MISC/pair_edip_multi.h
View File

@ -36,17 +36,17 @@ class PairEDIPMulti : public Pair {
protected:
struct Param {
double A, B;//coefficients for pair interaction I-J
double cutoffA;//cut-off distance for pair interaction I-J
double cutoffC;//lower cut-off distance for calculating Z_I
double alpha;//coefficient for calculating Z_I
double beta;//attractive term for pair I-J
double sigma;//cut-off coefficient for pair I-J
double rho;//pair I-J
double gamma;//coefficient for three-body interaction I-J-K
double eta, lambda;//coefficients for function h(l,Z)
double mu, Q0;//coefficients for function Q(Z)
double u1, u2, u3, u4;//coefficients for function tau(Z)
double A, B; // coefficients for pair interaction I-J
double cutoffA; // cut-off distance for pair interaction I-J
double cutoffC; // lower cut-off distance for calculating Z_I
double alpha; // coefficient for calculating Z_I
double beta; // attractive term for pair I-J
double sigma; // cut-off coefficient for pair I-J
double rho; // pair I-J
double gamma; // coefficient for three-body interaction I-J-K
double eta, lambda; // coefficients for function h(l,Z)
double mu, Q0; // coefficients for function Q(Z)
double u1, u2, u3, u4; // coefficients for function tau(Z)
double cutsq;
int ielement,jelement,kelement;
};
@ -62,10 +62,6 @@ class PairEDIPMulti : public Pair {
int maxparam; // max # of parameter sets
Param *params; // parameter set for an I-J-K interaction
// max number of interaction per atom for f(Z) environment potential
static const int leadDimInteractionList = 64;
void allocate();
void allocatePreLoops(void);
void deallocatePreLoops(void);

2
src/USER-MISC/pair_tersoff_table.h
View File

@ -43,7 +43,7 @@ class PairTersoffTable : public Pair {
void init_style();
double init_one(int, int);
static const int NPARAMS_PER_LINE = 17;
static constexpr int NPARAMS_PER_LINE = 17;
protected:
struct Param {

4
src/USER-OMP/dihedral_quadratic_omp.cpp
View File

@ -23,11 +23,13 @@
#include "neighbor.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOLERANCE 0.05
#define SMALL 0.001
@ -218,6 +220,8 @@ void DihedralQuadraticOMP::eval(int nfrom, int nto, ThrData * const thr)
siinv = 1.0/si;
double dphi = phi-phi0[type];
if (dphi > MY_PI) dphi -= 2*MY_PI;
else if (dphi < -MY_PI) dphi += 2*MY_PI;
p = k[type]*dphi;
pd = - 2.0 * p * siinv;
p = p * dphi;

126
src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp Normal file
View File

@ -0,0 +1,126 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "omp_compat.h"
#include "npair_half_size_multi_newtoff_omp.h"
#include "npair_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and other bins in stencil
multi-type stencil is itype dependent and is distance checked
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
// skip if i,j neighbor cutoff is less than bin distance
// stores own/own pairs only once
// stores own/ghost pairs on both procs
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
}

44
src/USER-OMP/npair_half_size_multi_newtoff_omp.h Normal file
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@ -0,0 +1,44 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newtoff/omp,
NPairHalfSizeMultiNewtoffOmp,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP |
NP_ORTHO | NP_TRI)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewtoffOmp : public NPair {
public:
NPairHalfSizeMultiNewtoffOmp(class LAMMPS *);
~NPairHalfSizeMultiNewtoffOmp() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

151
src/USER-OMP/npair_half_size_multi_newton_omp.cpp Normal file
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@ -0,0 +1,151 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "omp_compat.h"
#include "npair_half_size_multi_newton_omp.h"
#include "npair_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewtonOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// 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 and to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
// loop over all atoms in other bins in stencil, store every pair
// skip if i,j neighbor cutoff is less than bin distance
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
}

43
src/USER-OMP/npair_half_size_multi_newton_omp.h Normal file
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@ -0,0 +1,43 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newton/omp,
NPairHalfSizeMultiNewtonOmp,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewtonOmp : public NPair {
public:
NPairHalfSizeMultiNewtonOmp(class LAMMPS *);
~NPairHalfSizeMultiNewtonOmp() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

134
src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp Normal file
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@ -0,0 +1,134 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "omp_compat.h"
#include "npair_half_size_multi_newton_tri_omp.h"
#include "npair_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with Newton's 3rd law for triclinic
each owned atom i checks its own bin and other bins in triclinic stencil
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over all atoms in bins, including self, in stencil
// skip if i,j neighbor cutoff is less than bin distance
// bins below self are excluded from stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
}

43
src/USER-OMP/npair_half_size_multi_newton_tri_omp.h Normal file
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@ -0,0 +1,43 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newton/tri/omp,
NPairHalfSizeMultiNewtonTriOmp,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewtonTriOmp : public NPair {
public:
NPairHalfSizeMultiNewtonTriOmp(class LAMMPS *);
~NPairHalfSizeMultiNewtonTriOmp() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

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

@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
// max number of interaction per atom for f(Z) environment potential
#define leadDimInteractionList 64
static constexpr int leadDimInteractionList = 64;
/* ---------------------------------------------------------------------- */

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

@ -23,6 +23,8 @@
#include <cmath>
#include "omp_compat.h"
#include "pair_lj_cubic_const.h"
using namespace LAMMPS_NS;
using namespace PairLJCubicConstants;

1
src/USER-OMP/pair_zbl_omp.cpp
View File

@ -24,7 +24,6 @@
#include "omp_compat.h"
using namespace LAMMPS_NS;
using namespace PairZBLConstants;
/* ---------------------------------------------------------------------- */

11
src/USER-SMTBQ/pair_smtbq.cpp
View File

@ -72,17 +72,6 @@ using namespace MathSpecial;
#define PGDELTA 1
#define MAXNEIGH 24
/* ------------------------------------------------------------------------------------
Calculates the factorial of an integer n via recursion.
------------------------------------------------------------------------------------ */
static double factorial(int n)
{
if (n <= 1) return 1.0;
else return static_cast<double>(n)*factorial(n-1);
}
/* ---------------------------------------------------------------------- */
PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp)

92
src/balance.cpp
View File

@ -924,66 +924,66 @@ int Balance::shift()
i = 0;
while (i < np) {
if (split[i+1] - split[i] < close) {
j = i+1;
j = i+1;
// I,J = set of consecutive splits that are collectively too close
// if can expand set and not become too close to splits I-1 or J+1, do it
// else add split I-1 or J+1 to set and try again
// delta = size of expanded split set that will satisy criterion
// I,J = set of consecutive splits that are collectively too close
// if can expand set and not become too close to splits I-1 or J+1, do it
// else add split I-1 or J+1 to set and try again
// delta = size of expanded split set that will satisy criterion
while (1) {
delta = (j-i) * close;
midpt = 0.5 * (split[i]+split[j]);
start = midpt - 0.5*delta;
stop = midpt + 0.5*delta;
while (1) {
delta = (j-i) * close;
midpt = 0.5 * (split[i]+split[j]);
start = midpt - 0.5*delta;
stop = midpt + 0.5*delta;
if (i > 0) lbound = split[i-1] + close;
else lbound = 0.0;
if (j < np) ubound = split[j+1] - close;
else ubound = 1.0;
if (i > 0) lbound = split[i-1] + close;
else lbound = 0.0;
if (j < np) ubound = split[j+1] - close;
else ubound = 1.0;
// start/stop are within bounds, reset the splits
// start/stop are within bounds, reset the splits
if (start >= lbound && stop <= ubound) break;
if (start >= lbound && stop <= ubound) break;
// try a shift to either bound, reset the splits if delta fits
// these tests change start/stop
// try a shift to either bound, reset the splits if delta fits
// these tests change start/stop
if (start < lbound) {
start = lbound;
stop = start + delta;
if (stop <= ubound) break;
} else if (stop > ubound) {
stop = ubound;
start = stop - delta;
if (start >= lbound) break;
}
if (start < lbound) {
start = lbound;
stop = start + delta;
if (stop <= ubound) break;
} else if (stop > ubound) {
stop = ubound;
start = stop - delta;
if (start >= lbound) break;
}
// delta does not fit between lbound and ubound
// exit if can't expand set, else expand set
// if can expand in either direction,
// pick new split closest to current midpt of set
// delta does not fit between lbound and ubound
// exit if can't expand set, else expand set
// if can expand in either direction,
// pick new split closest to current midpt of set
if (i == 0 && j == np) {
start = 0.0; stop = 1.0;
break;
}
if (i == 0) j++;
else if (j == np) i--;
else if (midpt-lbound < ubound-midpt) i--;
else j++;
}
if (i == 0 && j == np) {
start = 0.0; stop = 1.0;
break;
}
if (i == 0) j++;
else if (j == np) i--;
else if (midpt-lbound < ubound-midpt) i--;
else j++;
}
// reset all splits between I,J inclusive to be equi-spaced
// reset all splits between I,J inclusive to be equi-spaced
spacing = (stop-start) / (j-i);
for (m = i; m <= j; m++)
split[m] = start + (m-i)*spacing;
spacing = (stop-start) / (j-i);
for (m = i; m <= j; m++)
split[m] = start + (m-i)*spacing;
if (j == np) split[np] = 1.0;
// continue testing beyond the J split
// continue testing beyond the J split
i = j+1;
i = j+1;
} else i++;
}

191
src/compute_orientorder_atom.cpp
View File

@ -23,6 +23,7 @@
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
@ -36,6 +37,8 @@
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#ifdef DBL_EPSILON
#define MY_EPSILON (10.0*DBL_EPSILON)
@ -708,191 +711,3 @@ void ComputeOrientOrderAtom::init_clebsch_gordan()
}
}
}
/* ----------------------------------------------------------------------
factorial n, wrapper for precomputed table
------------------------------------------------------------------------- */
double ComputeOrientOrderAtom::factorial(int n)
{
if (n < 0 || n > nmaxfactorial)
error->all(FLERR,fmt::format("Invalid argument to factorial {}", n));
return nfac_table[n];
}
/* ----------------------------------------------------------------------
factorial n table, size SNA::nmaxfactorial+1
------------------------------------------------------------------------- */
const double ComputeOrientOrderAtom::nfac_table[] = {
1,
1,
2,
6,
24,
120,
720,
5040,
40320,
362880,
3628800,
39916800,
479001600,
6227020800,
87178291200,
1307674368000,
20922789888000,
355687428096000,
6.402373705728e+15,
1.21645100408832e+17,
2.43290200817664e+18,
5.10909421717094e+19,
1.12400072777761e+21,
2.5852016738885e+22,
6.20448401733239e+23,
1.5511210043331e+25,
4.03291461126606e+26,
1.08888694504184e+28,
3.04888344611714e+29,
8.8417619937397e+30,
2.65252859812191e+32,
8.22283865417792e+33,
2.63130836933694e+35,
8.68331761881189e+36,
2.95232799039604e+38,
1.03331479663861e+40,
3.71993326789901e+41,
1.37637530912263e+43,
5.23022617466601e+44,
2.03978820811974e+46,
8.15915283247898e+47,
3.34525266131638e+49,
1.40500611775288e+51,
6.04152630633738e+52,
2.65827157478845e+54,
1.1962222086548e+56,
5.50262215981209e+57,
2.58623241511168e+59,
1.24139155925361e+61,
6.08281864034268e+62,
3.04140932017134e+64,
1.55111875328738e+66,
8.06581751709439e+67,
4.27488328406003e+69,
2.30843697339241e+71,
1.26964033536583e+73,
7.10998587804863e+74,
4.05269195048772e+76,
2.35056133128288e+78,
1.3868311854569e+80,
8.32098711274139e+81,
5.07580213877225e+83,
3.14699732603879e+85,
1.98260831540444e+87,
1.26886932185884e+89,
8.24765059208247e+90,
5.44344939077443e+92,
3.64711109181887e+94,
2.48003554243683e+96,
1.71122452428141e+98,
1.19785716699699e+100,
8.50478588567862e+101,
6.12344583768861e+103,
4.47011546151268e+105,
3.30788544151939e+107,
2.48091408113954e+109,
1.88549470166605e+111,
1.45183092028286e+113,
1.13242811782063e+115,
8.94618213078297e+116,
7.15694570462638e+118,
5.79712602074737e+120,
4.75364333701284e+122,
3.94552396972066e+124,
3.31424013456535e+126,
2.81710411438055e+128,
2.42270953836727e+130,
2.10775729837953e+132,
1.85482642257398e+134,
1.65079551609085e+136,
1.48571596448176e+138,
1.3520015276784e+140,
1.24384140546413e+142,
1.15677250708164e+144,
1.08736615665674e+146,
1.03299784882391e+148,
9.91677934870949e+149,
9.61927596824821e+151,
9.42689044888324e+153,
9.33262154439441e+155,
9.33262154439441e+157,
9.42594775983835e+159,
9.61446671503512e+161,
9.90290071648618e+163,
1.02990167451456e+166,
1.08139675824029e+168,
1.14628056373471e+170,
1.22652020319614e+172,
1.32464181945183e+174,
1.44385958320249e+176,
1.58824554152274e+178,
1.76295255109024e+180,
1.97450685722107e+182,
2.23119274865981e+184,
2.54355973347219e+186,
2.92509369349301e+188,
3.3931086844519e+190,
3.96993716080872e+192,
4.68452584975429e+194,
5.5745857612076e+196,
6.68950291344912e+198,
8.09429852527344e+200,
9.8750442008336e+202,
1.21463043670253e+205,
1.50614174151114e+207,
1.88267717688893e+209,
2.37217324288005e+211,
3.01266001845766e+213,
3.8562048236258e+215,
4.97450422247729e+217,
6.46685548922047e+219,
8.47158069087882e+221,
1.118248651196e+224,
1.48727070609069e+226,
1.99294274616152e+228,
2.69047270731805e+230,
3.65904288195255e+232,
5.01288874827499e+234,
6.91778647261949e+236,
9.61572319694109e+238,
1.34620124757175e+241,
1.89814375907617e+243,
2.69536413788816e+245,
3.85437071718007e+247,
5.5502938327393e+249,
8.04792605747199e+251,
1.17499720439091e+254,
1.72724589045464e+256,
2.55632391787286e+258,
3.80892263763057e+260,
5.71338395644585e+262,
8.62720977423323e+264,
1.31133588568345e+267,
2.00634390509568e+269,
3.08976961384735e+271,
4.78914290146339e+273,
7.47106292628289e+275,
1.17295687942641e+278,
1.85327186949373e+280,
2.94670227249504e+282,
4.71472363599206e+284,
7.59070505394721e+286,
1.22969421873945e+289,
2.0044015765453e+291,
3.28721858553429e+293,
5.42391066613159e+295,
9.00369170577843e+297,
1.503616514865e+300, // nmaxfactorial = 167
};

3
src/compute_orientorder_atom.h
View File

@ -56,9 +56,6 @@ class ComputeOrientOrderAtom : public Compute {
double polar_prefactor(int, int, double);
double associated_legendre(int, int, double);
static const int nmaxfactorial = 167;
static const double nfac_table[];
double factorial(int);
virtual void init_clebsch_gordan();
double *cglist; // Clebsch-Gordan coeffs
int idxcg_max;

51
src/fix.h
View File

@ -251,31 +251,32 @@ class Fix : protected Pointers {
};
namespace FixConst {
static const int INITIAL_INTEGRATE = 1<<0;
static const int POST_INTEGRATE = 1<<1;
static const int PRE_EXCHANGE = 1<<2;
static const int PRE_NEIGHBOR = 1<<3;
static const int POST_NEIGHBOR = 1<<4;
static const int PRE_FORCE = 1<<5;
static const int PRE_REVERSE = 1<<6;
static const int POST_FORCE = 1<<7;
static const int FINAL_INTEGRATE = 1<<8;
static const int END_OF_STEP = 1<<9;
static const int POST_RUN = 1<<10;
static const int THERMO_ENERGY = 1<<11;
static const int INITIAL_INTEGRATE_RESPA = 1<<12;
static const int POST_INTEGRATE_RESPA = 1<<13;
static const int PRE_FORCE_RESPA = 1<<14;
static const int POST_FORCE_RESPA = 1<<15;
static const int FINAL_INTEGRATE_RESPA = 1<<16;
static const int MIN_PRE_EXCHANGE = 1<<17;
static const int MIN_PRE_NEIGHBOR = 1<<18;
static const int MIN_POST_NEIGHBOR = 1<<19;
static const int MIN_PRE_FORCE = 1<<20;
static const int MIN_PRE_REVERSE = 1<<21;
static const int MIN_POST_FORCE = 1<<22;
static const int MIN_ENERGY = 1<<23;
static const int FIX_CONST_LAST = 1<<24;
enum {
INITIAL_INTEGRATE = 1<<0,
POST_INTEGRATE = 1<<1,
PRE_EXCHANGE = 1<<2,
PRE_NEIGHBOR = 1<<3,
POST_NEIGHBOR = 1<<4,
PRE_FORCE = 1<<5,
PRE_REVERSE = 1<<6,
POST_FORCE = 1<<7,
FINAL_INTEGRATE = 1<<8,
END_OF_STEP = 1<<9,
POST_RUN = 1<<10,
THERMO_ENERGY = 1<<11,
INITIAL_INTEGRATE_RESPA = 1<<12,
POST_INTEGRATE_RESPA = 1<<13,
PRE_FORCE_RESPA = 1<<14,
POST_FORCE_RESPA = 1<<15,
FINAL_INTEGRATE_RESPA = 1<<16,
MIN_PRE_EXCHANGE = 1<<17,
MIN_PRE_NEIGHBOR = 1<<18,
MIN_POST_NEIGHBOR = 1<<19,
MIN_PRE_FORCE = 1<<20,
MIN_PRE_REVERSE = 1<<21,
MIN_POST_FORCE = 1<<22,
MIN_ENERGY = 1<<23
};
}
}

7
src/fix_temp_csld.cpp
View File

@ -305,16 +305,17 @@ double FixTempCSLD::compute_scalar()
void FixTempCSLD::write_restart(FILE *fp)
{
int nsize = (98+2+3)*comm->nprocs+2; // pRNG state per proc + nprocs + energy
const int PRNGSIZE = 98+2+3;
int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy
double *list = nullptr;
if (comm->me == 0) {
list = new double[nsize];
list[0] = energy;
list[1] = comm->nprocs;
}
double state[103];
double state[PRNGSIZE];
random->get_state(state);
MPI_Gather(state,103,MPI_DOUBLE,list+2,103*comm->nprocs,MPI_DOUBLE,0,world);
MPI_Gather(state,PRNGSIZE,MPI_DOUBLE,list+2,PRNGSIZE,MPI_DOUBLE,0,world);
if (comm->me == 0) {
int size = nsize * sizeof(double);

7
src/fix_temp_csvr.cpp
View File

@ -338,16 +338,17 @@ double FixTempCSVR::compute_scalar()
void FixTempCSVR::write_restart(FILE *fp)
{
int nsize = (98+2+3)*comm->nprocs+2; // pRNG state per proc + nprocs + energy
const int PRNGSIZE = 98+2+3;
int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy
double *list = nullptr;
if (comm->me == 0) {
list = new double[nsize];
list[0] = energy;
list[1] = comm->nprocs;
}
double state[103];
double state[PRNGSIZE];
random->get_state(state);
MPI_Gather(state,103,MPI_DOUBLE,list+2,103*comm->nprocs,MPI_DOUBLE,0,world);
MPI_Gather(state,PRNGSIZE,MPI_DOUBLE,list+2,PRNGSIZE,MPI_DOUBLE,0,world);
if (comm->me == 0) {
int size = nsize * sizeof(double);

24
src/math_const.h
View File

@ -17,18 +17,18 @@
namespace LAMMPS_NS {
namespace MathConst {
static const double THIRD = 1.0/3.0;
static const double TWOTHIRDS = 2.0/3.0;
static const double MY_PI = 3.14159265358979323846; // pi
static const double MY_2PI = 6.28318530717958647692; // 2pi
static const double MY_3PI = 9.42477796076937971538; // 3pi
static const double MY_4PI = 12.56637061435917295384; // 4pi
static const double MY_PI2 = 1.57079632679489661923; // pi/2
static const double MY_PI4 = 0.78539816339744830962; // pi/4
static const double MY_PIS = 1.77245385090551602729; // sqrt(pi)
static const double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
static const double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
static const double MY_CBRT2 = 1.25992104989487316476; // 2*(1/3)
static constexpr double THIRD = 1.0/3.0;
static constexpr double TWOTHIRDS = 2.0/3.0;
static constexpr double MY_PI = 3.14159265358979323846; // pi
static constexpr double MY_2PI = 6.28318530717958647692; // 2pi
static constexpr double MY_3PI = 9.42477796076937971538; // 3pi
static constexpr double MY_4PI = 12.56637061435917295384; // 4pi
static constexpr double MY_PI2 = 1.57079632679489661923; // pi/2
static constexpr double MY_PI4 = 0.78539816339744830962; // pi/4
static constexpr double MY_PIS = 1.77245385090551602729; // sqrt(pi)
static constexpr double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
static constexpr double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
static constexpr double MY_CBRT2 = 1.25992104989487316476; // 2*(1/3)
}
}

194
src/math_special.cpp
View File

@ -1,9 +1,203 @@
#include "math_special.h"
#include <cmath>
#include <cstdint> // IWYU pragma: keep
#include <limits>
#include "error.h"
using namespace LAMMPS_NS;
static constexpr int nmaxfactorial = 167;
/* ----------------------------------------------------------------------
factorial n table, size nmaxfactorial+1
------------------------------------------------------------------------- */
static const double nfac_table[] = {
1,
1,
2,
6,
24,
120,
720,
5040,
40320,
362880,
3628800,
39916800,
479001600,
6227020800,
87178291200,
1307674368000,
20922789888000,
355687428096000,
6.402373705728e+15,
1.21645100408832e+17,
2.43290200817664e+18,
5.10909421717094e+19,
1.12400072777761e+21,
2.5852016738885e+22,
6.20448401733239e+23,
1.5511210043331e+25,
4.03291461126606e+26,
1.08888694504184e+28,
3.04888344611714e+29,
8.8417619937397e+30,
2.65252859812191e+32,
8.22283865417792e+33,
2.63130836933694e+35,
8.68331761881189e+36,
2.95232799039604e+38,
1.03331479663861e+40,
3.71993326789901e+41,
1.37637530912263e+43,
5.23022617466601e+44,
2.03978820811974e+46,
8.15915283247898e+47,
3.34525266131638e+49,
1.40500611775288e+51,
6.04152630633738e+52,
2.65827157478845e+54,
1.1962222086548e+56,
5.50262215981209e+57,
2.58623241511168e+59,
1.24139155925361e+61,
6.08281864034268e+62,
3.04140932017134e+64,
1.55111875328738e+66,
8.06581751709439e+67,
4.27488328406003e+69,
2.30843697339241e+71,
1.26964033536583e+73,
7.10998587804863e+74,
4.05269195048772e+76,
2.35056133128288e+78,
1.3868311854569e+80,
8.32098711274139e+81,
5.07580213877225e+83,
3.14699732603879e+85,
1.98260831540444e+87,
1.26886932185884e+89,
8.24765059208247e+90,
5.44344939077443e+92,
3.64711109181887e+94,
2.48003554243683e+96,
1.71122452428141e+98,
1.19785716699699e+100,
8.50478588567862e+101,
6.12344583768861e+103,
4.47011546151268e+105,
3.30788544151939e+107,
2.48091408113954e+109,
1.88549470166605e+111,
1.45183092028286e+113,
1.13242811782063e+115,
8.94618213078297e+116,
7.15694570462638e+118,
5.79712602074737e+120,
4.75364333701284e+122,
3.94552396972066e+124,
3.31424013456535e+126,
2.81710411438055e+128,
2.42270953836727e+130,
2.10775729837953e+132,
1.85482642257398e+134,
1.65079551609085e+136,
1.48571596448176e+138,
1.3520015276784e+140,
1.24384140546413e+142,
1.15677250708164e+144,
1.08736615665674e+146,
1.03299784882391e+148,
9.91677934870949e+149,
9.61927596824821e+151,
9.42689044888324e+153,
9.33262154439441e+155,
9.33262154439441e+157,
9.42594775983835e+159,
9.61446671503512e+161,
9.90290071648618e+163,
1.02990167451456e+166,
1.08139675824029e+168,
1.14628056373471e+170,
1.22652020319614e+172,
1.32464181945183e+174,
1.44385958320249e+176,
1.58824554152274e+178,
1.76295255109024e+180,
1.97450685722107e+182,
2.23119274865981e+184,
2.54355973347219e+186,
2.92509369349301e+188,
3.3931086844519e+190,
3.96993716080872e+192,
4.68452584975429e+194,
5.5745857612076e+196,
6.68950291344912e+198,
8.09429852527344e+200,
9.8750442008336e+202,
1.21463043670253e+205,
1.50614174151114e+207,
1.88267717688893e+209,
2.37217324288005e+211,
3.01266001845766e+213,
3.8562048236258e+215,
4.97450422247729e+217,
6.46685548922047e+219,
8.47158069087882e+221,
1.118248651196e+224,
1.48727070609069e+226,
1.99294274616152e+228,
2.69047270731805e+230,
3.65904288195255e+232,
5.01288874827499e+234,
6.91778647261949e+236,
9.61572319694109e+238,
1.34620124757175e+241,
1.89814375907617e+243,
2.69536413788816e+245,
3.85437071718007e+247,
5.5502938327393e+249,
8.04792605747199e+251,
1.17499720439091e+254,
1.72724589045464e+256,
2.55632391787286e+258,
3.80892263763057e+260,
5.71338395644585e+262,
8.62720977423323e+264,
1.31133588568345e+267,
2.00634390509568e+269,
3.08976961384735e+271,
4.78914290146339e+273,
7.47106292628289e+275,
1.17295687942641e+278,
1.85327186949373e+280,
2.94670227249504e+282,
4.71472363599206e+284,
7.59070505394721e+286,
1.22969421873945e+289,
2.0044015765453e+291,
3.28721858553429e+293,
5.42391066613159e+295,
9.00369170577843e+297,
1.503616514865e+300, // nmaxfactorial = 167
};
/* ----------------------------------------------------------------------
factorial n vial lookup from precomputed table
------------------------------------------------------------------------- */
double MathSpecial::factorial(const int n)
{
if (n < 0 || n > nmaxfactorial)
return std::numeric_limits<double>::quiet_NaN();
return nfac_table[n];
}
/* Library libcerf:
* Compute complex error functions, based on a new implementation of
* Faddeeva's w_of_z. Also provide Dawson and Voigt functions.

4
src/math_special.h
View File

@ -20,6 +20,10 @@ namespace LAMMPS_NS {
namespace MathSpecial {
// tabulated factorial function
extern double factorial(const int);
// support function for scaled error function complement
extern double erfcx_y100(const double y100);

88
src/neighbor.h
View File

@ -235,49 +235,55 @@ class Neighbor : protected Pointers {
};
namespace NeighConst {
static const int NB_INTEL = 1<<0;
static const int NB_KOKKOS_DEVICE = 1<<1;
static const int NB_KOKKOS_HOST = 1<<2;
static const int NB_SSA = 1<<3;
enum {
NB_INTEL = 1<<0,
NB_KOKKOS_DEVICE = 1<<1,
NB_KOKKOS_HOST = 1<<2,
NB_SSA = 1<<3
};
static const int NS_BIN = 1<<0;
static const int NS_MULTI = 1<<1;
static const int NS_HALF = 1<<2;
static const int NS_FULL = 1<<3;
static const int NS_2D = 1<<4;
static const int NS_3D = 1<<5;
static const int NS_NEWTON = 1<<6;
static const int NS_NEWTOFF = 1<<7;
static const int NS_ORTHO = 1<<8;
static const int NS_TRI = 1<<9;
static const int NS_GHOST = 1<<10;
static const int NS_SSA = 1<<11;
enum {
NS_BIN = 1<<0,
NS_MULTI = 1<<1,
NS_HALF = 1<<2,
NS_FULL = 1<<3,
NS_2D = 1<<4,
NS_3D = 1<<5,
NS_NEWTON = 1<<6,
NS_NEWTOFF = 1<<7,
NS_ORTHO = 1<<8,
NS_TRI = 1<<9,
NS_GHOST = 1<<10,
NS_SSA = 1<<11
};
static const int NP_NSQ = 1<<0;
static const int NP_BIN = 1<<1;
static const int NP_MULTI = 1<<2;
static const int NP_HALF = 1<<3;
static const int NP_FULL = 1<<4;
static const int NP_ORTHO = 1<<5;
static const int NP_TRI = 1<<6;
static const int NP_ATOMONLY = 1<<7;
static const int NP_MOLONLY = 1<<8;
static const int NP_NEWTON = 1<<9;
static const int NP_NEWTOFF = 1<<10;
static const int NP_GHOST = 1<<11;
static const int NP_SIZE = 1<<12;
static const int NP_ONESIDE = 1<<13;
static const int NP_RESPA = 1<<14;
static const int NP_BOND = 1<<15;
static const int NP_OMP = 1<<16;
static const int NP_INTEL = 1<<17;
static const int NP_KOKKOS_DEVICE = 1<<18;
static const int NP_KOKKOS_HOST = 1<<19;
static const int NP_SSA = 1<<20;
static const int NP_COPY = 1<<21;
static const int NP_SKIP = 1<<22;
static const int NP_HALF_FULL = 1<<23;
static const int NP_OFF2ON = 1<<24;
enum {
NP_NSQ = 1<<0,
NP_BIN = 1<<1,
NP_MULTI = 1<<2,
NP_HALF = 1<<3,
NP_FULL = 1<<4,
NP_ORTHO = 1<<5,
NP_TRI = 1<<6,
NP_ATOMONLY = 1<<7,
NP_MOLONLY = 1<<8,
NP_NEWTON = 1<<9,
NP_NEWTOFF = 1<<10,
NP_GHOST = 1<<11,
NP_SIZE = 1<<12,
NP_ONESIDE = 1<<13,
NP_RESPA = 1<<14,
NP_BOND = 1<<15,
NP_OMP = 1<<16,
NP_INTEL = 1<<17,
NP_KOKKOS_DEVICE = 1<<18,
NP_KOKKOS_HOST = 1<<19,
NP_SSA = 1<<20,
NP_COPY = 1<<21,
NP_SKIP = 1<<22,
NP_HALF_FULL = 1<<23,
NP_OFF2ON = 1<<24
};
}
}

117
src/npair_half_size_multi_newtoff.cpp Normal file
View File

@ -0,0 +1,117 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "npair_half_size_multi_newtoff.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and other bins in stencil
multi-type stencil is itype dependent and is distance checked
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewtoff::build(NeighList *list)
{
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int history = list->history;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int mask_history = 3 << SBBITS;
int inum = 0;
ipage->reset();
for (i = 0; i < nlocal; i++) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
// skip if i,j neighbor cutoff is less than bin distance
// stores own/own pairs only once
// stores own/ghost pairs on both procs
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}

46
src/npair_half_size_multi_newtoff.h Normal file
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@ -0,0 +1,46 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newtoff,
NPairHalfSizeMultiNewtoff,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewtoff : public NPair {
public:
NPairHalfSizeMultiNewtoff(class LAMMPS *);
~NPairHalfSizeMultiNewtoff() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Neighbor list overflow, boost neigh_modify one
UNDOCUMENTED
*/

143
src/npair_half_size_multi_newton.cpp Normal file
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@ -0,0 +1,143 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "npair_half_size_multi_newton.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewton::build(NeighList *list)
{
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int history = list->history;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int mask_history = 3 << SBBITS;
int inum = 0;
ipage->reset();
for (i = 0; i < nlocal; i++) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// 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 and to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
// loop over all atoms in other bins in stencil, store every pair
// skip if i,j neighbor cutoff is less than bin distance
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}

46
src/npair_half_size_multi_newton.h Normal file
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@ -0,0 +1,46 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newton,
NPairHalfSizeMultiNewton,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewton : public NPair {
public:
NPairHalfSizeMultiNewton(class LAMMPS *);
~NPairHalfSizeMultiNewton() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Neighbor list overflow, boost neigh_modify one
UNDOCUMENTED
*/

125
src/npair_half_size_multi_newton_tri.cpp Normal file
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@ -0,0 +1,125 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "npair_half_size_multi_newton_tri.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with Newton's 3rd law for triclinic
each owned atom i checks its own bin and other bins in triclinic stencil
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
{
int i,j,k,m,n,itype,jtype,ibin,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutdistsq;
int *neighptr,*s;
double *cutsq,*distsq;
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int history = list->history;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int mask_history = 3 << SBBITS;
int inum = 0;
ipage->reset();
for (i = 0; i < nlocal; i++) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over all atoms in bins, including self, in stencil
// skip if i,j neighbor cutoff is less than bin distance
// bins below self are excluded from stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutdistsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutdistsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}

46
src/npair_half_size_multi_newton_tri.h Normal file
View File

@ -0,0 +1,46 @@
/* -*- 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 NPAIR_CLASS
NPairStyle(half/size/multi/newton/tri,
NPairHalfSizeMultiNewtonTri,
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI)
#else
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H
#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfSizeMultiNewtonTri : public NPair {
public:
NPairHalfSizeMultiNewtonTri(class LAMMPS *);
~NPairHalfSizeMultiNewtonTri() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Neighbor list overflow, boost neigh_modify one
UNDOCUMENTED
*/

2
src/pair_coul_streitz.h
View File

@ -36,7 +36,7 @@ class PairCoulStreitz : public Pair {
double memory_usage();
virtual void *extract(const char *, int &);
static const int NPARAMS_PER_LINE = 6;
static constexpr int NPARAMS_PER_LINE = 6;
protected:
struct Param {

1
src/pair_lj_cubic.cpp
View File

@ -26,6 +26,7 @@
#include "memory.h"
#include "error.h"
#include "pair_lj_cubic_const.h"
using namespace LAMMPS_NS;
using namespace PairLJCubicConstants;

14
src/pair_lj_cubic.h
View File

@ -46,20 +46,6 @@ class PairLJCubic : public Pair {
void allocate();
};
namespace PairLJCubicConstants {
// LJ quantities scaled by epsilon and rmin = sigma*2^1/6
static const double RT6TWO = 1.1224621; // 2^1/6
static const double SS = 1.1086834; // inflection point (13/7)^1/6
static const double PHIS = -0.7869823; // energy at s
static const double DPHIDS = 2.6899009; // gradient at s
static const double A3 = 27.93357; // cubic coefficient
static const double SM = 1.5475375; // cubic cutoff = s*67/48
}
}
#endif

48
src/pair_lj_cubic_const.h Normal file
View File

@ -0,0 +1,48 @@
/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_LJ_CUBIC_CONST_H
#define LMP_PAIR_LJ_CUBIC_CONST_H
namespace LAMMPS_NS {
namespace PairLJCubicConstants {
// LJ quantities scaled by epsilon and rmin = sigma*2^1/6
static constexpr double RT6TWO = 1.1224620483093730; // 2^1/6
static constexpr double SS = 1.1086834179687215; // inflection point (13/7)^1/6
static constexpr double PHIS = -0.7869822485207097; // energy at s
static constexpr double DPHIDS = 2.6899008972047196; // gradient at s
static constexpr double A3 = 27.9335700460986445; // cubic coefficient
static constexpr double SM = 1.5475372709146737; // cubic cutoff = s*67/48}
}
}
#endif
// python script to compute the constants
//
// sixth = 1.0/6.0
// rmin = pow(2.0,sixth)
// rs = pow(26.0/7.0,sixth)
// ss = rs/rmin
// pow6 = pow(1.0/rs,6.0)
// phis = 4.0*pow6*(pow6-1.0)
// dpds = -24.0*pow6*(2.0*pow6-1.0)/rs*rmin
// a3 = 8.0*pow(dpds,3)/(9.0*phis*phis)
// sm = 67.0/48.0*ss
// print("static constexpr double RT6TWO = %19.16f; // 2^1/6" % rmin)
// print("static constexpr double SS = %19.16f; // inflection point (13/7)^1/6" % ss)
// print("static constexpr double PHIS = %19.16f; // energy at s" % phis)
// print("static constexpr double DPHIDS = %19.16f; // gradient at s" % dpds)
// print("static constexpr double A3 = %19.16f; // cubic coefficient" % a3)
// print("static constexpr double SM = %19.16f; // cubic cutoff = s*67/48" % sm)

7
src/pair_zbl.cpp
View File

@ -16,15 +16,18 @@
------------------------------------------------------------------------- */
#include "pair_zbl.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "pair_zbl_const.h"
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.

17
src/pair_zbl.h
View File

@ -54,23 +54,6 @@ class PairZBL : public Pair {
double d2zbldr2(double, int, int);
void set_coeff(int, int, double, double);
};
namespace PairZBLConstants {
// ZBL constants
static const double pzbl = 0.23;
static const double a0 = 0.46850;
static const double c1 = 0.02817;
static const double c2 = 0.28022;
static const double c3 = 0.50986;
static const double c4 = 0.18175;
static const double d1 = 0.20162;
static const double d2 = 0.40290;
static const double d3 = 0.94229;
static const double d4 = 3.19980;
}
}
#endif

34
src/pair_zbl_const.h Normal file
View File

@ -0,0 +1,34 @@
/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_ZBL_CONST_H
#define LMP_PAIR_ZBL_CONST_H
namespace LAMMPS_NS {
namespace PairZBLConstants {
// ZBL constants
static constexpr double pzbl = 0.23;
static constexpr double a0 = 0.46850;
static constexpr double c1 = 0.02817;
static constexpr double c2 = 0.28022;
static constexpr double c3 = 0.50986;
static constexpr double c4 = 0.18175;
static constexpr double d1 = 0.20162;
static constexpr double d2 = 0.40290;
static constexpr double d3 = 0.94229;
static constexpr double d4 = 3.19980;
}
}
#endif

2
src/text_file_reader.h
View File

@ -27,7 +27,7 @@ namespace LAMMPS_NS
class TextFileReader {
std::string filename;
std::string filetype;
static const int MAXLINE = 1024;
static constexpr int MAXLINE = 1024;
char line[MAXLINE];
FILE *fp;

14
unittest/c-library/test_library_mpi.cpp
View File

@ -173,7 +173,7 @@ TEST(MPI, multi_partition)
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &me);
const char *args[] = {"LAMMPS_test", "-log", "none", "-partition", "2x2",
const char *args[] = {"LAMMPS_test", "-log", "none", "-partition", "4x1",
"-echo", "screen", "-nocite", "-in", "none"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
@ -183,19 +183,15 @@ TEST(MPI, multi_partition)
lammps_command(lmp, "atom_style atomic");
lammps_command(lmp, "region box block 0 2 0 2 0 2");
lammps_command(lmp, "create_box 1 box");
lammps_command(lmp, "variable partition universe 1 2");
lammps_command(lmp, "variable partition universe 1 2 3 4");
EXPECT_EQ(lammps_extract_setting(lmp, "universe_size"), nprocs);
EXPECT_EQ(lammps_extract_setting(lmp, "universe_rank"), me);
EXPECT_EQ(lammps_extract_setting(lmp, "world_size"), nprocs / 2);
EXPECT_EQ(lammps_extract_setting(lmp, "world_rank"), me % 2);
EXPECT_EQ(lammps_extract_setting(lmp, "world_size"), 1);
EXPECT_EQ(lammps_extract_setting(lmp, "world_rank"), 0);
char *part_id = (char *)lammps_extract_variable(lmp, "partition", nullptr);
if (me < 2) {
ASSERT_THAT(part_id, StrEq("1"));
} else {
ASSERT_THAT(part_id, StrEq("2"));
}
ASSERT_THAT(part_id, StrEq(std::to_string(me+1)));
lammps_close(lmp);
};

2
unittest/force-styles/tests/fix-timestep-oneway.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:41 202
epsilon: 2e-14
epsilon: 4e-14
prerequisites: ! |
atom full
fix oneway

128
unittest/force-styles/tests/mol-pair-lj_cubic.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:15 202
epsilon: 2e-13
lammps_version: 30 Nov 2020
date_generated: Fri Dec 18 22:30:42 202
epsilon: 1e-13
prerequisites: ! |
atom full
pair lj/cubic
@ -19,72 +19,72 @@ pair_coeff: ! |
5 5 0.015 3.1
extract: ! ""
natoms: 29
init_vdwl: 166.005266308562
init_vdwl: 166.005266338502
init_coul: 0
init_stress: ! |2-
4.5860676757908186e+02 4.8091912919212928e+02 1.0767204080701006e+03 -2.1005546139122362e+02 -2.9491286717936713e+00 1.6145675857120941e+02
4.5860676760613336e+02 4.8091912923656065e+02 1.0767204080957010e+03 -2.1005546139899724e+02 -2.9491286649299440e+00 1.6145675855773089e+02
init_forces: ! |2
1 9.1849370411551270e+00 7.6268937957720553e+01 6.1726872441625311e+01
2 2.2858712118514426e+01 1.8809274242266209e+01 -2.6905829837199740e+01
3 -3.2016987482543328e+01 -9.4135849525427091e+01 -3.4799279593035926e+01
4 -5.5341015869901478e-01 1.5206999898436971e-01 -3.9418368928369890e-01
5 -1.8042057425348118e-01 -3.0459951056385326e-01 8.7068483241007189e-01
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