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initial version of pair style hybrid/molecular

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This commit is contained in:
Axel Kohlmeyer
2024-06-09 07:02:18 -04:00
parent 7ef9a93a75
commit 91b9308d4f
14 changed files with 103 additions and 44 deletions
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2
doc/src/Commands_pair.rst
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@ -26,6 +26,7 @@ OPT.
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/molecular <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`kim <pair_kim>`
@ -34,7 +35,6 @@ OPT.
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`

42
doc/src/pair_hybrid.rst
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@ -1,5 +1,6 @@
.. index:: pair_style hybrid
.. index:: pair_style hybrid/kk
.. index:: pair_style hybrid/molecular
.. index:: pair_style hybrid/overlay
.. index:: pair_style hybrid/overlay/kk
.. index:: pair_style hybrid/scaled
@ -9,6 +10,9 @@ pair_style hybrid command
Accelerator Variants: *hybrid/kk*
pair_style hybrid/molecular command
===================================
pair_style hybrid/overlay command
=================================
@ -23,6 +27,7 @@ Syntax
.. code-block:: LAMMPS
pair_style hybrid style1 args style2 args ...
pair_style hybrid/molecular factor1 style1 args factor2 style 2 args
pair_style hybrid/overlay style1 args style2 args ...
pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
@ -47,6 +52,10 @@ Examples
pair_coeff * * tersoff Si.tersoff Si
pair_coeff * * sw Si.sw Si
pair_style hybrid/molecular lj/cut 2.5 lj/cut 2.5
pair_coeff * * lj/cut 1 1.0 1.0
pair_coeff * * lj/cut 2 1.5 1.0
variable one equal ramp(1.0,0.0)
variable two equal 1.0-v_one
pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
@ -56,17 +65,26 @@ Examples
Description
"""""""""""
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
use of multiple pair styles in one simulation. With the *hybrid* style,
exactly one pair style is assigned to each pair of atom types. With the
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
be assigned to each pair of atom types. The assignment of pair styles
to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command.
The major difference between the *hybrid/overlay* and *hybrid/scaled*
styles is that the *hybrid/scaled* adds a scale factor for each
sub-style contribution to forces, energies and stresses. Because of the
added complexity, the *hybrid/scaled* style has more overhead and thus
may be slower than *hybrid/overlay*.
The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled*
styles enable the use of multiple pair styles in one simulation. With
the *hybrid* style, exactly one pair style is assigned to each pair of
atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one
or more pair styles can be assigned to each pair of atom types. With
the hybrid/molecular style, pair styles are assigned to either intra-
or inter-molecular interactions.
The assignment of pair styles to type pairs is made via the
:doc:`pair_coeff <pair_coeff>` command. The major difference between
the *hybrid/overlay* and *hybrid/scaled* styles is that the
*hybrid/scaled* adds a scale factor for each sub-style contribution to
forces, energies and stresses. Because of the added complexity, the
*hybrid/scaled* style has more overhead and thus may be slower than
*hybrid/overlay*.
The *hybrid/molecular* pair style accepts *only* two sub-styles: the
first is assigned to intra-molecular interactions (i.e. both atoms
have the same molecule ID), the second to inter-molecular interactions
(i.e. interacting atoms have different molecule IDs).
Here are two examples of hybrid simulations. The *hybrid* style could
be used for a simulation of a metal droplet on a LJ surface. The metal
@ -476,6 +494,8 @@ the same or else LAMMPS will generate an error.
Pair style *hybrid/scaled* currently only works for non-accelerated
pair styles and pair styles from the OPT package.
Pair style *hybrid/molecular* is not compatible with manybody potentials.
When using pair styles from the GPU package they must not be listed
multiple times. LAMMPS will detect this and abort.

1
doc/src/pair_style.rst
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@ -108,6 +108,7 @@ accelerated styles exist.
* :doc:`none <pair_none>` - turn off pairwise interactions
* :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
* :doc:`hybrid/molecular <pair_hybrid>` - different pair styles for intra- and inter-molecular interactions
* :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
* :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
* :doc:`zero <pair_zero>` - neighbor list but no interactions

19
src/neigh_list.cpp
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@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq)
copy = nq->copy;
trim = nq->trim;
id = nq->id;
molskip = nq->molskip;
if (nq->copy) {
listcopy = neighbor->lists[nq->copylist];
@ -157,14 +158,16 @@ void NeighList::post_constructor(NeighRequest *nq)
if (nq->skip) {
listskip = neighbor->lists[nq->skiplist];
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j];
if (!molskip) {
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j];
}
}
if (nq->halffull)

1
src/neigh_list.h
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@ -46,6 +46,7 @@ class NeighList : protected Pointers {
int kk2cpu; // 1 if this list is copied from Kokkos to CPU
int copymode; // 1 if this is a Kokkos on-device copy
int id; // copied from neighbor list request
int molskip; // 1/2 if this is an intra-/inter-molecular skip list
// data structs to store neighbor pairs I,J and associated values

9
src/neigh_request.cpp
View File

@ -76,6 +76,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
skip = 0;
iskip = nullptr;
ijskip = nullptr;
molskip = 0;
// only set when command = 1;
@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other)
int NeighRequest::same_skip(NeighRequest *other)
{
if (molskip != other->molskip) return 0;
const int ntypes = atom->ntypes;
int same = 1;
@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip)
ijskip = _ijskip;
}
void NeighRequest::set_molskip(int _molskip)
{
skip = 1;
molskip = _molskip;
}
void NeighRequest::enable_full()
{
half = 0;

5
src/neigh_request.h
View File

@ -29,6 +29,9 @@ class NeighRequest : protected Pointers {
friend class NPairSkipTrimIntel;
friend class FixIntel;
public:
enum { REGULAR, INTRA, INTER };
protected:
void *requestor; // class that made request
int requestor_instance; // instance of that class (only Fix, Compute, Pair)
@ -88,6 +91,7 @@ class NeighRequest : protected Pointers {
int skip; // 1 if this list skips atom types from another list
int *iskip; // iskip[i] if atoms of type I are not in list
int **ijskip; // ijskip[i][j] if pairs of type I,J are not in list
int molskip; // 0 reqular list, 1 keep only intra-molecular entries, 2 keep inter-molecular
// command_style only set if command = 1
// allows print_pair_info() to access command name
@ -137,6 +141,7 @@ class NeighRequest : protected Pointers {
void set_kokkos_device(int);
void set_kokkos_host(int);
void set_skip(int *, int **);
void set_molskip(int);
void enable_full();
void enable_ghost();
void enable_intel();

15
src/neighbor.cpp
View File

@ -1800,10 +1800,17 @@ void Neighbor::print_pairwise_info()
else
out += fmt::format(", half/full from ({})",rq->halffulllist+1);
} else if (rq->skip) {
if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", skip from ({})",rq->skiplist+1);
if (rq->molskip) {
if (rq->trim)
out += fmt::format(", molskip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", molskip from ({})",rq->skiplist+1);
} else {
if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", skip from ({})",rq->skiplist+1);
}
}
out += "\n";

3
src/neighbor.h
View File

@ -334,7 +334,8 @@ namespace NeighConst {
NP_HALF_FULL = 1 << 23,
NP_OFF2ON = 1 << 24,
NP_MULTI_OLD = 1 << 25,
NP_TRIM = 1 << 26
NP_TRIM = 1 << 26,
NP_INTRA = 1 << 27
};
enum {

12
src/npair_halffull.h
View File

@ -53,13 +53,13 @@ typedef NPairHalffull<1, 0, 0> NPairHalffullNewton;
NPairStyle(halffull/newton/skip,
NPairHalffullNewton,
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_ORTHO | NP_SKIP);
NP_ORTHO | NP_SKIP | NP_INTRA);
typedef NPairHalffull<1, 1, 0> NPairHalffullNewtonTri;
NPairStyle(halffull/newton/skip/tri,
NPairHalffullNewtonTri,
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_TRI | NP_SKIP);
NP_TRI | NP_SKIP | NP_INTRA);
typedef NPairHalffull<0, 0, 1> NPairHalffullTrimNewtoff;
NPairStyle(halffull/trim/newtoff,
@ -71,7 +71,7 @@ typedef NPairHalffull<0, 0, 1> NPairHalffullTrimNewtoff;
NPairStyle(halffull/trim/newtoff/skip,
NPairHalffullTrimNewtoff,
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM);
NP_ORTHO | NP_TRI | NP_SKIP | NP_INTRA | NP_TRIM);
typedef NPairHalffull<0, 0, 1> NPairHalffullTrimNewtoff;
NPairStyle(halffull/trim/newtoff/ghost,
@ -83,7 +83,7 @@ typedef NPairHalffull<0, 0, 1> NPairHalffullTrimNewtoff;
NPairStyle(halffull/trim/newtoff/skip/ghost,
NPairHalffullTrimNewtoff,
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST | NP_TRIM);
NP_ORTHO | NP_TRI | NP_SKIP | NP_INTRA | NP_GHOST | NP_TRIM);
typedef NPairHalffull<1, 0, 1> NPairHalffullTrimNewton;
NPairStyle(halffull/trim/newton,
@ -101,13 +101,13 @@ typedef NPairHalffull<1, 0, 1> NPairHalffullTrimNewton;
NPairStyle(halffull/trim/newton/skip,
NPairHalffullTrimNewton,
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_ORTHO | NP_SKIP | NP_TRIM);
NP_ORTHO | NP_SKIP | NP_INTRA | NP_TRIM);
typedef NPairHalffull<1, 1, 1> NPairHalffullTrimNewtonTri;
NPairStyle(halffull/trim/newton/tri/skip,
NPairHalffullTrimNewtonTri,
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_TRI | NP_SKIP | NP_TRIM);
NP_TRI | NP_SKIP | NP_INTRA | NP_TRIM);
// clang-format on
#else

10
src/npair_skip.cpp
View File

@ -17,6 +17,7 @@
#include "error.h"
#include "my_page.h"
#include "neigh_list.h"
#include "neigh_request.h"
using namespace LAMMPS_NS;
@ -41,11 +42,13 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
int *type = atom->type;
int nlocal = atom->nlocal;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int molskip = list->molskip;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
@ -71,7 +74,8 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
for (ii = 0; ii < num_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
if (!molskip && iskip[itype]) continue;
if (TRIM) {
xtmp = x[i][0];
@ -90,7 +94,9 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
if (TRIM) {
delx = xtmp - x[j][0];

14
src/npair_skip.h
View File

@ -16,41 +16,43 @@
typedef NPairSkipTemp<0> NPairSkip;
NPairStyle(skip,
NPairSkip,
NP_SKIP | NP_HALF | NP_FULL |
NP_SKIP | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairSkipTemp<0> NPairSkip;
NPairStyle(skip/ghost,
NPairSkip,
NP_SKIP | NP_HALF | NP_FULL |
NP_SKIP | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST);
typedef NPairSkipTemp<0> NPairSkipSize;
NPairStyle(skip/half/size,
NPairSkipSize,
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairSkipTemp<1> NPairSkipTrim;
NPairStyle(skip/trim,
NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL |
NP_SKIP | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM);
typedef NPairSkipTemp<1> NPairSkipTrim;
NPairStyle(skip/ghost/trim,
NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL |
NP_SKIP | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM);
typedef NPairSkipTemp<1> NPairSkipTrimSize;
NPairStyle(skip/trim/half/size,
NPairSkipTrimSize,
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM);
// clang-format on

4
src/npair_skip_respa.h
View File

@ -16,14 +16,14 @@
typedef NPairSkipRespaTemp<0> NPairSkipRespa;
NPairStyle(skip/half/respa,
NPairSkipRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairSkipRespaTemp<1> NPairSkipTrimRespa;
NPairStyle(skip/trim/half/respa,
NPairSkipTrimRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_INTRA |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM);

8
src/pair_hybrid.cpp
View File

@ -321,11 +321,12 @@ void PairHybrid::settings(int narg, char **arg)
iarg = 0;
nstyles = 0;
const std::string mystyle = force->pair_style;
while (iarg < narg) {
if (utils::strmatch(arg[iarg],"^hybrid"))
error->all(FLERR,"Pair style hybrid cannot have hybrid as a sub-style");
error->all(FLERR,"Pair style {} cannot have hybrid as a sub-style", mystyle);
if (strcmp(arg[iarg],"none") == 0)
error->all(FLERR,"Pair style hybrid cannot have none as a sub-style");
error->all(FLERR,"Pair style {} cannot have none as a sub-style", mystyle);
styles[nstyles] = force->new_pair(arg[iarg],1,dummy);
keywords[nstyles] = force->store_style(arg[iarg],0);
@ -345,6 +346,9 @@ void PairHybrid::settings(int narg, char **arg)
nstyles++;
}
if (utils::strmatch(mystyle,"^hybrid/molecular") && (nstyles != 2))
error->all(FLERR, "Pair style {} must have exactly two sub-styles", mystyle);
delete[] cutmax_style;
cutmax_style = new double[nstyles];
memset(cutmax_style, 0, nstyles*sizeof(double));