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Merge pull request #4191 from akohlmey/pair-hybrid-molecule

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Add new pair style hybrid/molecular
This commit is contained in:
Axel Kohlmeyer
2024-06-19 00:49:37 -04:00
committed by GitHub
parent b9f8a5b811 71b38521c5
commit 37572225f4
22 changed files with 577 additions and 68 deletions
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8
doc/src/Commands_pair.rst
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@ -25,16 +25,16 @@ OPT.
* :doc:`none <pair_none>` * :doc:`none <pair_none>`
* :doc:`zero <pair_zero>` * :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>` * :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>` * :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>` * :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>` * :doc:`kim <pair_kim>`
* :doc:`list <pair_list>` * :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>` * :doc:`tracker <pair_tracker>`
* *
* *
* *
*
* :doc:`adp (ko) <pair_adp>` * :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>` * :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>` * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`

54
doc/src/pair_hybrid.rst
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@ -1,28 +1,41 @@
.. index:: pair_style hybrid .. index:: pair_style hybrid
.. index:: pair_style hybrid/kk .. index:: pair_style hybrid/kk
.. index:: pair_style hybrid/omp
.. index:: pair_style hybrid/molecular
.. index:: pair_style hybrid/molecular/omp
.. index:: pair_style hybrid/overlay .. index:: pair_style hybrid/overlay
.. index:: pair_style hybrid/overlay/omp
.. index:: pair_style hybrid/overlay/kk .. index:: pair_style hybrid/overlay/kk
.. index:: pair_style hybrid/scaled .. index:: pair_style hybrid/scaled
.. index:: pair_style hybrid/scaled/omp
pair_style hybrid command pair_style hybrid command
========================= =========================
Accelerator Variants: *hybrid/kk* Accelerator Variants: *hybrid/kk*, *hybrid/omp*
pair_style hybrid/molecular command
===================================
Accelerator Variant: *hybrid/molecular/omp*
pair_style hybrid/overlay command pair_style hybrid/overlay command
================================= =================================
Accelerator Variants: *hybrid/overlay/kk* Accelerator Variants: *hybrid/overlay/kk*, *hybrid/overlay/omp*
pair_style hybrid/scaled command pair_style hybrid/scaled command
================================== ==================================
Accelerator Variant: *hybrid/scaled/omp*
Syntax Syntax
"""""" """"""
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style hybrid style1 args style2 args ... 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/overlay style1 args style2 args ...
pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ... pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
@ -47,6 +60,10 @@ Examples
pair_coeff * * tersoff Si.tersoff Si pair_coeff * * tersoff Si.tersoff Si
pair_coeff * * sw Si.sw 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 one equal ramp(1.0,0.0)
variable two equal 1.0-v_one variable two equal 1.0-v_one
pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
@ -56,17 +73,26 @@ Examples
Description Description
""""""""""" """""""""""
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled*
use of multiple pair styles in one simulation. With the *hybrid* style, styles enable the use of multiple pair styles in one simulation. With
exactly one pair style is assigned to each pair of atom types. With the the *hybrid* style, exactly one pair style is assigned to each pair of
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one
be assigned to each pair of atom types. The assignment of pair styles or more pair styles can be assigned to each pair of atom types. With
to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command. the hybrid/molecular style, pair styles are assigned to either intra-
The major difference between the *hybrid/overlay* and *hybrid/scaled* or inter-molecular interactions.
styles is that the *hybrid/scaled* adds a scale factor for each
sub-style contribution to forces, energies and stresses. Because of the The assignment of pair styles to type pairs is made via the
added complexity, the *hybrid/scaled* style has more overhead and thus :doc:`pair_coeff <pair_coeff>` command. The major difference between
may be slower than *hybrid/overlay*. 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 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 be used for a simulation of a metal droplet on a LJ surface. The metal
@ -476,6 +502,8 @@ the same or else LAMMPS will generate an error.
Pair style *hybrid/scaled* currently only works for non-accelerated Pair style *hybrid/scaled* currently only works for non-accelerated
pair styles and pair styles from the OPT package. 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 When using pair styles from the GPU package they must not be listed
multiple times. LAMMPS will detect this and abort. 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:`none <pair_none>` - turn off pairwise interactions
* :doc:`hybrid <pair_hybrid>` - multiple styles of 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/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
* :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions * :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
* :doc:`zero <pair_zero>` - neighbor list but no interactions * :doc:`zero <pair_zero>` - neighbor list but no interactions

22
src/INTEL/npair_skip_intel.cpp
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@ -74,9 +74,13 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int nlocal = atom->nlocal; const int nlocal = atom->nlocal;
const int e_nall = nlocal + atom->nghost; const int e_nall = nlocal + atom->nghost;
const int * _noalias const type = atom->type; const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist; int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh; int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh; const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -110,7 +114,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) { for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii]; const int i = ilist_skip[ii];
const int itype = type[i]; const int itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
int n = 0; int n = 0;
int *neighptr = ipage.vget(); int *neighptr = ipage.vget();
@ -142,7 +146,11 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int jj = 0; jj < jnum; jj++) { for (int jj = 0; jj < jnum; jj++) {
const int joriginal = jlist[jj]; const int joriginal = jlist[jj];
const int j = joriginal & NEIGHMASK; const int j = joriginal & NEIGHMASK;
if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; 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;
neighptr[n++] = joriginal;
} }
} }
@ -269,9 +277,13 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int e_nall = nlocal + atom->nghost; const int e_nall = nlocal + atom->nghost;
const ATOM_T * _noalias const x = buffers->get_x(); const ATOM_T * _noalias const x = buffers->get_x();
const int * _noalias const type = atom->type; const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist; int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh; int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh; const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -306,7 +318,7 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) { for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii]; const int i = ilist_skip[ii];
const int itype = type[i]; const int itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
const flt_t xtmp = x[i].x; const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y; const flt_t ytmp = x[i].y;
@ -370,7 +382,9 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int j = joriginal & NEIGHMASK; const int j = joriginal & NEIGHMASK;
int addme = 1; int addme = 1;
if (ijskip[itype][type[j]]) addme = 0; if (!molskip && ijskip[itype][type[j]]) addme = 0;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) addme = 0;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) addme = 0;
// trim to shorter cutoff // trim to shorter cutoff

8
src/OPENMP/fix_omp.cpp
View File

@ -229,7 +229,13 @@ void FixOMP::init()
check_hybrid = 0; \ check_hybrid = 0; \
if (force->name) { \ if (force->name) { \
if ( (strcmp(force->name ## _style,"hybrid") == 0) || \ if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \ (strcmp(force->name ## _style,"hybrid/overlay") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular") == 0) || \
(strcmp(force->name ## _style,"hybrid/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular/omp") == 0) ) \
check_hybrid=1; \ check_hybrid=1; \
if (force->name->suffix_flag & Suffix::OMP) { \ if (force->name->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \ last_force_name = (const char *) #name; \

34
src/OPENMP/npair_skip_omp.h
View File

@ -19,14 +19,12 @@
NPairStyle(skip/omp, NPairStyle(skip/omp,
NPairSkip, NPairSkip,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/respa/omp, NPairStyle(skip/half/respa/omp,
NPairSkipRespa, NPairSkipRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/size/omp, NPairStyle(skip/half/size/omp,
@ -36,32 +34,27 @@ NPairStyle(skip/half/size/omp,
NPairStyle(skip/size/off2on/omp, NPairStyle(skip/size/off2on/omp,
NPairSkipSizeOff2on, NPairSkipSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/size/off2on/oneside/omp, NPairStyle(skip/size/off2on/oneside/omp,
NPairSkipSizeOff2onOneside, NPairSkipSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/ghost/omp, NPairStyle(skip/ghost/omp,
NPairSkip, NPairSkip,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST);
NPairStyle(skip/trim/omp, NPairStyle(skip/trim/omp,
NPairSkipTrim, NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/respa/omp, NPairStyle(skip/trim/half/respa/omp,
NPairSkipTrimRespa, NPairSkipTrimRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/size/omp, NPairStyle(skip/trim/half/size/omp,
@ -71,20 +64,17 @@ NPairStyle(skip/trim/half/size/omp,
NPairStyle(skip/trim/size/off2on/omp, NPairStyle(skip/trim/size/off2on/omp,
NPairSkipTrimSizeOff2on, NPairSkipTrimSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/size/off2on/oneside/omp, NPairStyle(skip/trim/size/off2on/oneside/omp,
NPairSkipTrimSizeOff2onOneside, NPairSkipTrimSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/ghost/omp, NPairStyle(skip/trim/ghost/omp,
NPairSkipTrim, NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST);
// clang-format off // clang-format off
#endif #endif

3
src/neigh_list.cpp
View File

@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq)
copy = nq->copy; copy = nq->copy;
trim = nq->trim; trim = nq->trim;
id = nq->id; id = nq->id;
molskip = nq->molskip;
if (nq->copy) { if (nq->copy) {
listcopy = neighbor->lists[nq->copylist]; listcopy = neighbor->lists[nq->copylist];
@ -157,6 +158,7 @@ void NeighList::post_constructor(NeighRequest *nq)
if (nq->skip) { if (nq->skip) {
listskip = neighbor->lists[nq->skiplist]; listskip = neighbor->lists[nq->skiplist];
if (!molskip) {
int ntypes = atom->ntypes; int ntypes = atom->ntypes;
iskip = new int[ntypes+1]; iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip"); memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
@ -166,6 +168,7 @@ void NeighList::post_constructor(NeighRequest *nq)
for (j = 1; j <= ntypes; j++) for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j]; ijskip[i][j] = nq->ijskip[i][j];
} }
}
if (nq->halffull) if (nq->halffull)
listfull = neighbor->lists[nq->halffulllist]; listfull = neighbor->lists[nq->halffulllist];

1
src/neigh_list.h
View File

@ -46,6 +46,7 @@ class NeighList : protected Pointers {
int kk2cpu; // 1 if this list is copied from Kokkos to CPU int kk2cpu; // 1 if this list is copied from Kokkos to CPU
int copymode; // 1 if this is a Kokkos on-device copy int copymode; // 1 if this is a Kokkos on-device copy
int id; // copied from neighbor list request 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 // 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; skip = 0;
iskip = nullptr; iskip = nullptr;
ijskip = nullptr; ijskip = nullptr;
molskip = REGULAR;
// only set when command = 1; // only set when command = 1;
@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other)
int NeighRequest::same_skip(NeighRequest *other) int NeighRequest::same_skip(NeighRequest *other)
{ {
if (molskip != other->molskip) return 0;
const int ntypes = atom->ntypes; const int ntypes = atom->ntypes;
int same = 1; int same = 1;
@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip)
ijskip = _ijskip; ijskip = _ijskip;
} }
void NeighRequest::set_molskip(int _molskip)
{
skip = 1;
molskip = _molskip;
}
void NeighRequest::enable_full() void NeighRequest::enable_full()
{ {
half = 0; half = 0;

5
src/neigh_request.h
View File

@ -29,6 +29,9 @@ class NeighRequest : protected Pointers {
friend class NPairSkipTrimIntel; friend class NPairSkipTrimIntel;
friend class FixIntel; friend class FixIntel;
public:
enum { REGULAR, INTRA, INTER };
protected: protected:
void *requestor; // class that made request void *requestor; // class that made request
int requestor_instance; // instance of that class (only Fix, Compute, Pair) 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 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 *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 **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 // command_style only set if command = 1
// allows print_pair_info() to access command name // allows print_pair_info() to access command name
@ -137,6 +141,7 @@ class NeighRequest : protected Pointers {
void set_kokkos_device(int); void set_kokkos_device(int);
void set_kokkos_host(int); void set_kokkos_host(int);
void set_skip(int *, int **); void set_skip(int *, int **);
void set_molskip(int);
void enable_full(); void enable_full();
void enable_ghost(); void enable_ghost();
void enable_intel(); void enable_intel();

7
src/neighbor.cpp
View File

@ -1800,11 +1800,18 @@ void Neighbor::print_pairwise_info()
else else
out += fmt::format(", half/full from ({})",rq->halffulllist+1); out += fmt::format(", half/full from ({})",rq->halffulllist+1);
} else if (rq->skip) { } else if (rq->skip) {
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) if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1); out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else else
out += fmt::format(", skip from ({})",rq->skiplist+1); out += fmt::format(", skip from ({})",rq->skiplist+1);
} }
}
out += "\n"; out += "\n";
// list of neigh list attributes // list of neigh list attributes

10
src/npair_skip.cpp
View File

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

6
src/npair_skip.h
View File

@ -30,7 +30,8 @@ NPairStyle(skip/ghost,
typedef NPairSkipTemp<0> NPairSkipSize; typedef NPairSkipTemp<0> NPairSkipSize;
NPairStyle(skip/half/size, NPairStyle(skip/half/size,
NPairSkipSize, 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_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairSkipTemp<1> NPairSkipTrim; typedef NPairSkipTemp<1> NPairSkipTrim;
@ -50,7 +51,8 @@ NPairStyle(skip/ghost/trim,
typedef NPairSkipTemp<1> NPairSkipTrimSize; typedef NPairSkipTemp<1> NPairSkipTrimSize;
NPairStyle(skip/trim/half/size, NPairStyle(skip/trim/half/size,
NPairSkipTrimSize, 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_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM);
// clang-format on // clang-format on

17
src/npair_skip_respa.cpp
View File

@ -18,6 +18,7 @@
#include "error.h" #include "error.h"
#include "my_page.h" #include "my_page.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -39,11 +40,13 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
int *neighptr, *jlist, *neighptr_inner, *neighptr_middle; int *neighptr, *jlist, *neighptr_inner, *neighptr_middle;
int *type = atom->type; int *type = atom->type;
tagint *molecule = atom->molecule;
int *ilist = list->ilist; int *ilist = list->ilist;
int *numneigh = list->numneigh; int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh; int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage; MyPage<int> *ipage = list->ipage;
int molskip = list->molskip;
int *ilist_skip = list->listskip->ilist; int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh; int *numneigh_skip = list->listskip->numneigh;
@ -90,7 +93,7 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (ii = 0; ii < inum_skip; ii++) { for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii]; i = ilist_skip[ii];
itype = type[i]; itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
if (TRIM) { if (TRIM) {
xtmp = x[i][0]; xtmp = x[i][0];
@ -114,7 +117,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; 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) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];
@ -135,7 +140,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; 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) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];
@ -157,7 +164,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; 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) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];

11
src/pair_hybrid.cpp
View File

@ -321,11 +321,12 @@ void PairHybrid::settings(int narg, char **arg)
iarg = 0; iarg = 0;
nstyles = 0; nstyles = 0;
const std::string mystyle = force->pair_style;
while (iarg < narg) { while (iarg < narg) {
if (utils::strmatch(arg[iarg],"^hybrid")) 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) 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); styles[nstyles] = force->new_pair(arg[iarg],1,dummy);
keywords[nstyles] = force->store_style(arg[iarg],0); keywords[nstyles] = force->store_style(arg[iarg],0);
@ -345,6 +346,9 @@ void PairHybrid::settings(int narg, char **arg)
nstyles++; nstyles++;
} }
if (utils::strmatch(mystyle,"^hybrid/molecular") && (nstyles != 2))
error->all(FLERR, "Pair style {} must have exactly two sub-styles", mystyle);
delete[] cutmax_style; delete[] cutmax_style;
cutmax_style = new double[nstyles]; cutmax_style = new double[nstyles];
memset(cutmax_style, 0, nstyles*sizeof(double)); memset(cutmax_style, 0, nstyles*sizeof(double));
@ -394,8 +398,7 @@ void PairHybrid::flags()
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward); if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse); if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,styles[m]->comm_reverse_off);
styles[m]->comm_reverse_off);
} }
// single_enable = 1 if all sub-styles are set // single_enable = 1 if all sub-styles are set

1
src/pair_hybrid.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid,PairHybrid); PairStyle(hybrid,PairHybrid);
PairStyle(hybrid/omp,PairHybrid);
// clang-format on // clang-format on
#else #else

162
src/pair_hybrid_molecular.cpp Normal file
View File

@ -0,0 +1,162 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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 "pair_hybrid_molecular.h"
#include "atom.h"
#include "error.h"
#include "neigh_request.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairHybridMolecular::PairHybridMolecular(LAMMPS *lmp) : PairHybridOverlay(lmp) {}
/* ----------------------------------------------------------------------
modify neighbor list requests
------------------------------------------------------------------------- */
void PairHybridMolecular::init_style()
{
if (!atom->molecule_flag)
error->all(FLERR, "Pair style hybrid/molecular requires atom attribute molecule");
if (manybody_flag)
error->all(FLERR, "Pair style hybrid/molecular is not compatible with manybody potentials");
PairHybridOverlay::init_style();
// modify neighbor list requests
bool first = true;
for (auto &request : neighbor->get_pair_requests()) {
if (first) {
request->set_molskip(NeighRequest::INTRA);
first = false;
} else {
request->set_molskip(NeighRequest::INTER);
}
}
born_matrix_enable = 0;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairHybridMolecular::init_one(int i, int j)
{
// if I,J is not set explicitly:
// perform mixing only if I,I sub-style = J,J sub-style
// plus I,I and J,J need the same number of substyles
if (setflag[i][j] == 0) {
if (nmap[i][i] != nmap[j][j])
error->one(FLERR,"All pair coeffs are not set");
int num = 0;
for (int k = 0; k < nmap[i][i]; ++k) {
for (int l = 0; l < nmap[j][j]; ++l) {
if (map[i][i][k] == map[j][j][l]) {
map[i][j][num] = map[i][i][k];
++num;
nmap[i][j] = num;
}
}
}
if (nmap[i][i] != nmap[i][j])
error->one(FLERR,"All pair coeffs are not set");
}
nmap[j][i] = nmap[i][j];
// call init/mixing for all sub-styles of I,J
// set cutsq in sub-style just as Pair::init() does via call to init_one()
// set cutghost for I,J and J,I just as sub-style does
// sum tail corrections for I,J
// return max cutoff of all sub-styles assigned to I,J
// if no sub-styles assigned to I,J (pair_coeff none), cutmax = 0.0 returned
double cutmax = 0.0;
cutghost[i][j] = cutghost[j][i] = 0.0;
if (tail_flag) etail_ij = ptail_ij = 0.0;
for (int k = 0; k < nmap[i][j]; k++) {
map[j][i][k] = map[i][j][k];
double cut = styles[map[i][j][k]]->init_one(i,j);
if (styles[map[i][j][k]]->did_mix) did_mix = true;
styles[map[i][j][k]]->cutsq[i][j] = styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
if (styles[map[i][j][k]]->ghostneigh)
cutghost[i][j] = cutghost[j][i] = MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
if (tail_flag) {
etail_ij += styles[map[i][j][k]]->etail_ij;
ptail_ij += styles[map[i][j][k]]->ptail_ij;
}
cutmax = MAX(cutmax,cut);
int istyle;
for (istyle = 0; istyle < nstyles; istyle++)
if (styles[istyle] == styles[map[i][j][k]]) break;
if (styles[istyle]->trim_flag) {
if (cut > cutmax_style[istyle]) {
cutmax_style[istyle] = cut;
for (auto &request : neighbor->get_pair_requests()) {
if (styles[istyle] == request->get_requestor()) {
request->set_cutoff(cutmax_style[istyle]);
break;
}
}
}
}
}
return cutmax;
}
/* ----------------------------------------------------------------------
call sub-style to compute single interaction
error if sub-style does not support single() call
since overlay could have multiple sub-styles, sum results explicitly
------------------------------------------------------------------------- */
double PairHybridMolecular::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &fforce)
{
if (nmap[itype][jtype] == 0)
error->one(FLERR,"Invoked pair single() on sub-style none");
double fone;
fforce = 0.0;
double esum = 0.0;
if (nmap[itype][jtype] == 2) {
int m = 0;
if (atom->molecule[i] != atom->molecule[j]) m = 1;
const int mystyle = map[itype][jtype][m];
if (rsq < styles[mystyle]->cutsq[itype][jtype]) {
if (styles[mystyle]->single_enable == 0)
error->one(FLERR,"Pair hybrid/molecular sub-style {} does not support single() call",
keywords[mystyle]);
if ((special_lj[mystyle] != nullptr) || (special_coul[mystyle] != nullptr))
error->one(FLERR,"Pair hybrid/molecular single() calls do not support per sub-style "
"special bond values");
esum += styles[mystyle]->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone);
fforce += fone;
}
}
if (single_extra) copy_svector(itype,jtype);
return esum;
}

41
src/pair_hybrid_molecular.h Normal file
View File

@ -0,0 +1,41 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(hybrid/molecular,PairHybridMolecular);
PairStyle(hybrid/molecular/omp,PairHybridMolecular);
// clang-format on
#else
#ifndef LMP_PAIR_HYBRID_MOLECULAR_H
#define LMP_PAIR_HYBRID_MOLECULAR_H
#include "pair_hybrid_overlay.h"
namespace LAMMPS_NS {
class PairHybridMolecular : public PairHybridOverlay {
public:
PairHybridMolecular(class LAMMPS *);
void init_style() override;
double init_one(int, int) override;
double single(int, int, int, int, double, double, double, double &) override;
};
} // namespace LAMMPS_NS
#endif
#endif

1
src/pair_hybrid_overlay.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid/overlay,PairHybridOverlay); PairStyle(hybrid/overlay,PairHybridOverlay);
PairStyle(hybrid/overlay/omp,PairHybridOverlay);
// clang-format on // clang-format on
#else #else

1
src/pair_hybrid_scaled.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid/scaled,PairHybridScaled); PairStyle(hybrid/scaled,PairHybridScaled);
PairStyle(hybrid/scaled/omp,PairHybridScaled);
// clang-format on // clang-format on
#else #else

100
unittest/force-styles/tests/mol-pair-hybrid_molecular.yaml Normal file
View File

@ -0,0 +1,100 @@
---
lammps_version: 17 Apr 2024
tags:
date_generated: Sun Jun 9 11:41:13 2024
epsilon: 1e-13
skip_tests:
prerequisites: ! |
atom full
pair lj/cut
pair hybrid/molecular
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify shift yes
input_file: in.fourmol
pair_style: hybrid/molecular lj/cut 8.0 lj/cut 8.0
pair_coeff: ! |
1 1 lj/cut 1 0.02 2.5
2 2 lj/cut 1 0.005 1.0
2 4 lj/cut 1 0.005 0.5
3 3 lj/cut 1 0.02 3.2
4 4 lj/cut 1 0.015 3.1
5 5 lj/cut 1 0.015 3.1
1 1 lj/cut 2 0.02 2.5
2 2 lj/cut 2 0.005 1.0
2 4 lj/cut 2 0.005 0.5
3 3 lj/cut 2 0.02 3.2
4 4 lj/cut 2 0.015 3.1
5 5 lj/cut 2 0.015 3.1
extract: ! ""
natoms: 29
init_vdwl: 749.2470096189497
init_coul: 0
init_stress: ! |2-
2.1793857186503237e+03 2.1988957679770601e+03 4.6653994738862348e+03 -7.5956544622684351e+02 2.4751393539193327e+01 6.6652061873806679e+02
init_forces: ! |2
1 -2.3333390274530565e+01 2.6994567613591136e+02 3.3272827850621587e+02
2 1.5828554630423909e+02 1.3025008843536872e+02 -1.8629682358915150e+02
3 -1.3528903744071786e+02 -3.8704313350789641e+02 -1.4568978426110147e+02
4 -7.8711096705734178e+00 2.1350518625352004e+00 -5.5954532185292400e+00
5 -2.5176757267276137e+00 -4.0521510680612876e+00 1.2152704057983799e+01
6 -8.3190665562047559e+02 9.6394165349388811e+02 1.1509101492424440e+03
7 5.8203416066164465e+01 -3.3609013622052356e+02 -1.7179626006587687e+03
8 1.4451392646293456e+02 -1.0927476052490437e+02 3.9990594285329479e+02
9 7.9156945283109025e+01 8.5273009784086469e+01 3.5032175698457496e+02
10 5.3118875219106917e+02 -6.1040990846582008e+02 -1.8355872692632028e+02
11 -2.3530157265571860e+00 -5.9077640075588906e+00 -9.6590723956614433e+00
12 1.7527155197359406e+01 1.0633119514682473e+01 -7.9254397903886158e+00
13 8.0986409580712841e+00 -3.2098088269317300e+00 -1.4896399871387667e-01
14 -3.3852721291218524e+00 6.8636181224987947e-01 -8.7507190862837803e+00
15 -2.0454999188607306e-01 8.4846165523012136e+00 3.0131615419840623e+00
16 4.6326331471561195e+02 -3.3087730492363477e+02 -1.1893030175606582e+03
17 -4.5334322060634048e+02 3.1554297967975305e+02 1.2058423415744451e+03
18 -1.8862629870158503e-02 -3.3402022492930034e-02 3.1000492146377390e-02
19 3.1843079948447594e-04 -2.3918628211596124e-04 1.7427252652160224e-03
20 -9.9760831169755002e-04 -1.0209184785886856e-03 3.6910973051849135e-04
21 -7.1566158640374354e+01 -8.1615716383825756e+01 2.2589571940670788e+02
22 -1.0808840769631149e+02 -2.6193799449067580e+01 -1.6957912849816358e+02
23 1.7964463850759611e+02 1.0782102722442450e+02 -5.6305812731665995e+01
24 3.6591423637378952e+01 -2.1181597497621908e+02 1.1218307103182993e+02
25 -1.4851496072162067e+02 2.3907129270267117e+01 -1.2485640694398953e+02
26 1.1191134671510581e+02 1.8789783424990625e+02 1.2650143102803206e+01
27 5.1810412832328005e+01 -2.2705468907750404e+02 9.0849153441059272e+01
28 -1.8041315533250560e+02 7.7534079082878250e+01 -1.2206962452216493e+02
29 1.2861063251415737e+02 1.4952718246094852e+02 3.1216040111076957e+01
run_vdwl: 719.4532389988315
run_coul: 0
run_stress: ! |2-
2.1330157554553725e+03 2.1547730555430494e+03 4.3976512412988704e+03 -7.3873325485023713e+02 4.1743707190785464e+01 6.2788040986774649e+02
run_forces: ! |2
1 -2.0299419744961813e+01 2.6686193379336868e+02 3.2358785871037435e+02
2 1.5298617928501707e+02 1.2596516341411086e+02 -1.7961292655320207e+02
3 -1.3353630670276331e+02 -3.7923748676909099e+02 -1.4291839777232488e+02
4 -7.8374717836014449e+00 2.1276610789788282e+00 -5.5845014473593917e+00
5 -2.5014258629959465e+00 -4.0250131424457543e+00 1.2103512372172734e+01
6 -8.0681466162480240e+02 9.2165651041424792e+02 1.0270802401119468e+03
7 5.5780302775854636e+01 -3.1117544157318952e+02 -1.5746997989226002e+03
8 1.3452983973683914e+02 -1.0064660034658647e+02 3.8851792520911863e+02
9 7.6746213900459239e+01 8.2501469902247337e+01 3.3944351209160595e+02
10 5.2128033526109800e+02 -5.9920098832868109e+02 -1.8126029871233905e+02
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27 5.0800867695850577e+01 -2.2296598219372004e+02 8.8607407764830413e+01
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29 1.2614900659680345e+02 1.4694257504728049e+02 3.0893400701043564e+01
...

119
unittest/force-styles/tests/mol-pair-hybrid_molecular_lj_morse.yaml Normal file
View File

@ -0,0 +1,119 @@
---
lammps_version: 17 Apr 2024
tags:
date_generated: Sun Jun 9 11:41:13 2024
epsilon: 1e-13
skip_tests:
prerequisites: ! |
atom full
pair lj/cut
pair morse
pair hybrid/molecular
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify shift yes
input_file: in.fourmol
pair_style: hybrid/molecular lj/cut 8.0 morse 8.0
pair_coeff: ! |
1 1 lj/cut 0.02 2.5
1 2 lj/cut 0.01 1.75
1 3 lj/cut 0.02 2.85
1 4 lj/cut 0.01732050807568877293 2.8
1 5 lj/cut 0.01732050807568877293 2.8
2 2 lj/cut 0.005 1.0
2 3 lj/cut 0.01 2.1
2 4 lj/cut 0.005 0.5
2 5 lj/cut 0.00866025403784438646 2.05
3 3 lj/cut 0.02 3.2
3 4 lj/cut 0.01732050807568877293 3.15
3 5 lj/cut 0.01732050807568877293 3.15
4 4 lj/cut 0.015 3.1
4 5 lj/cut 0.015 3.1
5 5 lj/cut 0.015 3.1
1 1 morse 0.0202798941614106 2.78203488021395 2.725417159299
1 2 morse 0.0101167811264648 3.9793050302425 1.90749569018897
1 3 morse 0.0202934330695928 2.43948720203264 3.10711749999622
1 4 morse 0.0175731334238374 2.48316585521317 3.05258880102438
1 5 morse 0.0175731334238374 2.48316585521317 3.05258880102438
2 2 morse 0.00503064360487288 6.98433077606902 1.08960295117864
2 3 morse 0.0101296013842819 3.31380153807866 2.28919067558352
2 4 morse 0.00497405122588691 14.0508902925745 0.544416409093563
2 5 morse 0.00877114211614446 3.39491256196178 2.23466262511073
3 3 morse 0.0203039874239943 2.17204344301477 3.48881895084762
3 4 morse 0.0175825321440736 2.20660439192238 3.43428999287994
3 5 morse 0.0175825321440736 2.20660439192238 3.43428999287994
4 4 morse 0.0152259201379927 2.24227873774009 3.37976131582396
4 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396
5 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396
extract: ! ""
natoms: 29
init_vdwl: 642.2857035487534
init_coul: 0
init_stress: ! |2-
1.5446101412530770e+03 1.7762864877230827e+03 4.3406629723991382e+03 -2.4168966825090698e+02 -4.2399281241000449e+02 1.0313398732648857e+03
init_forces: ! |2
1 -2.3337658999820331e+01 2.6994849929388920e+02 3.3272731927204762e+02
2 1.5828475525620013e+02 1.3025198646645657e+02 -1.8629727921784635e+02
3 -1.3530883593401191e+02 -3.8702990176780906e+02 -1.4568955729804821e+02
4 -7.8720974048138279e+00 2.1357285334450031e+00 -5.5956697614574145e+00
5 -2.5179872246085657e+00 -4.0521698308193113e+00 1.2152426584580066e+01
6 -1.0627539753780246e+02 3.7096636535889553e+02 1.6577829288882351e+03
7 6.2545311732649182e+01 -3.3857732069504033e+02 -1.7085638850072914e+03
8 -5.8544805218664203e+02 4.8619364551174579e+02 -1.1637016110669298e+02
9 7.9157108381891348e+01 8.5271268694585373e+01 3.5031950365280102e+02
10 5.3119792393751504e+02 -6.1042010285634149e+02 -1.8355328074325874e+02
11 -2.3525975498215241e+00 -5.9087312467830966e+00 -9.6592450379633981e+00
12 1.7514418718210869e+01 1.0633490551535797e+01 -7.9269392455530774e+00
13 8.0989976759274995e+00 -3.2092537736156967e+00 -1.4857368826935238e-01
14 -3.3831155658252769e+00 6.8583230320825528e-01 -8.7521044176224088e+00
15 -2.0078689909299524e-01 8.4842702953333049e+00 3.0127255727602438e+00
16 4.6326713730462569e+02 -3.3088113342819690e+02 -1.1892994362776039e+03
17 -4.5333858978430715e+02 3.1553830929611308e+02 1.2058459850635415e+03
18 -2.0452760511035117e-02 -3.1643654311568722e-02 2.7038063904994043e-02
19 6.7683676563436612e-04 5.5257878746558435e-04 3.4368881128008698e-04
20 -7.2687428125721442e-04 -6.4369255876917293e-04 -7.3055429537143658e-05
21 -7.1559739956792001e+01 -8.1623086552077027e+01 2.2588907386171752e+02
22 -1.0808827580116072e+02 -2.6193999003846525e+01 -1.6957935616989226e+02
23 1.7964485683675787e+02 1.0782085824265097e+02 -5.6306005220676077e+01
24 3.6592705490564995e+01 -2.1181065162415683e+02 1.1218892889291895e+02
25 -1.4851386780240065e+02 2.3908077402265249e+01 -1.2485428291933182e+02
26 1.1191162087301427e+02 1.8789805761651786e+02 1.2650515090480996e+01
27 5.1805674347396028e+01 -2.2705907095144718e+02 9.0852216146745278e+01
28 -1.8041330407833553e+02 7.7533936594765862e+01 -1.2206953762508090e+02
29 1.2861029896870866e+02 1.4952683033680830e+02 3.1216382013473979e+01
run_vdwl: 612.532027437114
run_coul: 0
run_stress: ! |2-
1.5079612443981077e+03 1.7300922919292559e+03 4.0645404509935297e+03 -2.2501656863720930e+02 -3.8440649220519191e+02 9.6872117407090468e+02
run_forces: ! |2
1 -2.0303664163328520e+01 2.6686344032747223e+02 3.2358595259116754e+02
2 1.5298537986232245e+02 1.2596704781215615e+02 -1.7961336269199933e+02
3 -1.3340899705451542e+02 -3.7937983996408559e+02 -1.4304731523709151e+02
4 -7.8384621494638589e+00 2.1283385602122546e+00 -5.5847156581558837e+00
5 -2.5017213737297879e+00 -4.0250398342732856e+00 1.2103221315331954e+01
6 -1.0069389067343234e+02 3.4070704568948952e+02 1.4995989516904360e+03
7 5.6637967265264535e+01 -3.0800622792471370e+02 -1.5506690902144287e+03
8 -5.6211472712331181e+02 4.6807109251305587e+02 -1.0712697415342610e+02
9 7.6069407842570087e+01 8.0619386602314336e+01 3.3418245682682038e+02
10 5.1153094792744940e+02 -5.8811350830044319e+02 -1.7678443640175220e+02
11 -2.3568347685072353e+00 -5.8621926046697821e+00 -9.6044928327397194e+00
12 1.7464493846680174e+01 1.0623724119993449e+01 -8.0428896399820058e+00
13 8.0533880511151636e+00 -3.1750913604087598e+00 -1.4579751155151741e-01
14 -3.3394709175794697e+00 6.6440083564233665e-01 -8.6358918170724337e+00
15 -2.1889102849274136e-01 8.5021207266300767e+00 3.0365920030191385e+00
16 4.3476429812120438e+02 -3.1171100998816553e+02 -1.1135203700101538e+03
17 -4.2469867717957146e+02 2.9615706504039451e+02 1.1302529422580635e+03
18 -2.0438484585882859e-02 -3.1629705308846789e-02 2.7018991453856001e-02
19 6.6852492737214141e-04 5.4625495751892833e-04 3.4152455215868423e-04
20 -7.1620896561888831e-04 -6.3500663583982407e-04 -7.1700429767679216e-05
21 -7.0484355349417541e+01 -7.9756579011007801e+01 2.2170349595393003e+02
22 -1.0638710558378827e+02 -2.5949713015442118e+01 -1.6645620880910886e+02
23 1.7686828769914484e+02 1.0571007956441812e+02 -5.5243556600722584e+01
24 3.8207315780355771e+01 -2.1022299522635379e+02 1.1261302962088173e+02
25 -1.4918780612527124e+02 2.3763111781582175e+01 -1.2548982817638399e+02
26 1.1097093258138914e+02 1.8645536456663984e+02 1.2861936841695268e+01
27 5.0796145560529055e+01 -2.2297034959629724e+02 8.8610475497234873e+01
28 -1.7694213444502824e+02 7.6029840540845129e+01 -1.1950515191029582e+02
29 1.2614865956603674e+02 1.4694220660200173e+02 3.0893738250707873e+01
...