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Merge branch 'reset-molecules' into write-bonus-data

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This commit is contained in:
Axel Kohlmeyer
2020-07-10 10:25:08 -04:00
parent 8102045fdb 0c89b517a5
commit df63d4147d
34 changed files with 1203 additions and 168 deletions
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3
doc/src/Commands_all.rst
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@ -101,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

3
doc/src/commands_list.rst
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@ -88,7 +88,8 @@ Commands
region
replicate
rerun
reset_ids
reset_atom_ids
reset_mol_ids
reset_timestep
restart
run

68
doc/src/compute_cluster_atom.rst
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@ -15,12 +15,18 @@ Syntax
.. parsed-literal::
compute ID group-ID cluster/atom cutoff
compute ID group-ID fragment/atom
compute ID group-ID fragment/atom keyword value ...
compute ID group-ID aggregate/atom cutoff
* ID, group-ID are documented in :doc:`compute <compute>` command
* *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command
* cutoff = distance within which to label atoms as part of same cluster (distance units)
* zero or more keyword/value pairs may be appended to *fragment/atom*
* keyword = *single*
.. parsed-literal::
*single* value = *yes* or *no* to treat single atoms (no bonds) as fragments
Examples
""""""""
@ -29,27 +35,36 @@ Examples
compute 1 all cluster/atom 3.5
compute 1 all fragment/atom
compute 1 all fragment/atom single no
compute 1 all aggregate/atom 3.5
Description
"""""""""""
Define a computation that assigns each atom a cluster, fragment,
or aggregate ID.
Define a computation that assigns each atom a cluster, fragment, or
aggregate ID. Only atoms in the compute group are clustered and
assigned cluster IDs. Atoms not in the compute group are assigned an
ID = 0.
A cluster is defined as a set of atoms, each of which is within the
cutoff distance from one or more other atoms in the cluster. If an
atom has no neighbors within the cutoff distance, then it is a 1-atom
cluster.
A fragment is similarly defined as a set of atoms, each of
which has an explicit bond (i.e. defined via a :doc:`data file <read_data>`,
the :doc:`create_bonds <create_bonds>` command, or through fixes like
:doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
or :doc:`fix bond/break <fix_bond_break>`). The cluster ID or fragment ID
of every atom in the cluster will be set to the smallest atom ID of any atom
in the cluster or fragment, respectively.
A fragment is similarly defined as a set of atoms, each of which has a
bond to another atom in the fragment. Bonds can be defined initially
via the :doc:`data file <read_data>` or :doc:`create_bonds
<create_bonds>` commands, or dynamically by fixes which create or
break bonds like :doc:`fix bond/react <fix_bond_react>`, :doc:`fix
bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
or :doc:`fix bond/break <fix_bond_break>`. The cluster ID or fragment
ID of every atom in the cluster will be set to the smallest atom ID of
any atom in the cluster or fragment, respectively.
For the *fragment/atom* style, the *single* keyword determines whether
single atoms (not bonded to another atom) are treated as one-atom
fragments or not, based on the *yes* or *no* setting. If the setting
is *no* (the default), their fragment IDs are set to 0.
An aggregate is defined by combining the rules for clusters and
fragments, i.e. a set of atoms, where each of it is within the cutoff
@ -57,19 +72,11 @@ distance from one or more atoms within a fragment that is part of
the same cluster. This measure can be used to track molecular assemblies
like micelles.
Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
For fragments, only bonds where **both** atoms of the bond are included
in the compute group are assigned to fragments, so that only fragments
are detected where **all** atoms are in the compute group. Thus atoms
may be included in the compute group, yes still have a fragment ID of 0.
For computes *cluster/atom* and *aggregate/atom* the neighbor list needed
to compute this quantity is constructed each time the calculation is
performed (i.e. each time a snapshot of atoms is dumped). Thus it can be
inefficient to compute/dump this quantity too frequently or to have
multiple compute/dump commands, each of a *cluster/atom* or
*aggregate/atom* style.
For computes *cluster/atom* and *aggregate/atom* a neighbor list
needed to compute cluster IDs is constructed each time the compute is
invoked. Thus it can be inefficient to compute/dump this quantity too
frequently or to have multiple *cluster/atom* or *aggregate/atom*
style computes.
.. note::
@ -89,6 +96,14 @@ multiple compute/dump commands, each of a *cluster/atom* or
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
.. note::
For the compute fragment/atom style, each fragment is identified
using the current bond topology. This will not account for bonds
broken by the :doc:`bond_style quartic <bond_quartic>` command
because it does not perform a full update of the bond topology data
structures within LAMMPS.
**Output info:**
This compute calculates a per-atom vector, which can be accessed by
@ -107,4 +122,7 @@ Related commands
:doc:`compute coord/atom <compute_coord_atom>`
**Default:** none
**Default:**
The default for fragment/atom is single no.

4
doc/src/delete_atoms.rst
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@ -89,7 +89,7 @@ number of atoms in the system. Note that this is not done for
molecular systems (see the :doc:`atom_style <atom_style>` command),
regardless of the *compress* setting, since it would foul up the bond
connectivity that has already been assigned. However, the
:doc:`reset_ids <reset_ids>` command can be used after this command to
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
accomplish the same thing.
Note that the re-assignment of IDs is not really a compression, where
@ -157,7 +157,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
Related commands
""""""""""""""""
:doc:`create_atoms <create_atoms>`, :doc:`reset_ids <reset_ids>`
:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
Default
"""""""

14
doc/src/reset_ids.rst → doc/src/reset_atom_ids.rst
View File

@ -1,14 +1,14 @@
.. index:: reset_ids
.. index:: reset_atom_ids
reset_ids command
=================
reset_atom_ids command
======================
Syntax
""""""
.. code-block:: LAMMPS
reset_ids keyword values ...
reset_atom_ids keyword values ...
* zero or more keyword/value pairs may be appended
* keyword = *sort*
@ -22,8 +22,8 @@ Examples
.. code-block:: LAMMPS
reset_ids
reset_ids sort yes
reset_atom_ids
reset_atom_ids sort yes
Description
"""""""""""
@ -77,7 +77,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
that are owned by other processors. The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue.
Or you can define a pair style before using this command. If you do
the former, you should unset the comm_modify cutoff after using
reset_ids so that subsequent communication is not inefficient.
reset_atom_ids so that subsequent communication is not inefficient.
Restrictions
""""""""""""

116
doc/src/reset_mol_ids.rst Normal file
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@ -0,0 +1,116 @@
.. index:: reset_mol_ids
reset_mol_ids command
=====================
Syntax
""""""
.. parsed-literal::
reset_mol_ids group-ID keyword value ...
* group-ID = ID of group of atoms whose molecule IDs will be reset
* zero or more keyword/value pairs may be appended
* keyword = *compress* or *offset* or *single*
.. parsed-literal::
*compress* value = *yes* or *no*
*offset* value = *Noffset* >= -1
*single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
Examples
""""""""
.. code-block:: LAMMPS
reset_mol_ids all
reset_mol_ids all offset 10 single yes
reset_mol_ids solvent compress yes offset 100
reset_mol_ids solvent compress no
Description
"""""""""""
Reset molecule IDs for a group of atoms based on current bond
connectivity. This will typically create a new set of molecule IDs
for atoms in the group. Only molecule IDs for atoms in the specified
group are reset; molecule IDs for atoms not in the group are not
changed.
For purposes of this operation, molecules are identified by the current
bond connectivity in the system, which may or may not be consistent with
the current molecule IDs. A molecule in this context is a set of atoms
connected to each other with explicit bonds. The specific algorithm
used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
Once the molecules are identified and a new molecule ID computed for
each, this command will update the current molecule ID for all atoms in
the group with the new molecule ID. Note that if the group excludes
atoms within molecules, one (physical) molecule may become two or more
(logical) molecules. For example if the group excludes atoms in the
middle of a linear chain, then each end of the chain is considered an
independent molecule and will be assigned a different molecule ID.
This can be a useful operation to perform after running reactive
molecular dynamics run with :doc:`fix bond/react <fix_bond_react>`,
:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
<fix_bond_break>`, all of which can change molecule topologies. It can
also be useful after molecules have been deleted with the
:doc:`delete_atoms <delete_atoms>` command or after a simulation which
has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
command.
The *compress* keyword determines how new molecule IDs are computed. If
the setting is *yes* (the default) and there are N molecules in the
group, the new molecule IDs will be a set of N contiguous values. See
the *offset* keyword for details on selecting the range of these values.
If the setting is *no*, the molecule ID of every atom in the molecule
will be set to the smallest atom ID of any atom in the molecule.
The *single* keyword determines whether single atoms (not bonded to
another atom) are treated as one-atom molecules or not, based on the
*yes* or *no* setting. If the setting is *no* (the default), their
molecule IDs are set to 0. This setting can be important if the new
molecule IDs will be used as input to other commands such as
:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
rigid molecule <fix_rigid>`.
The *offset* keyword is only used if the *compress* setting is *yes*.
Its default value is *Noffset* = -1. In that case, if the specified
group is *all*, then the new compressed molecule IDs will range from 1
to N. If the specified group is not *all* and the largest molecule ID
of atoms outside that group is M, then the new compressed molecule IDs will
range from M+1 to M+N, to avoid collision with existing molecule
IDs. If an *Noffset* >= 0 is specified, then the new compressed
molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N. If the group
is not *all* there may be collisions with the molecule IDs of other atoms.
.. note::
The same as explained for the :doc:`compute fragment/atom
<compute_cluster_atom>` command, molecules are identified using the
current bond topology. This will not account for bonds broken by
the :doc:`bond_style quartic <bond_quartic>` command because it
does not perform a full update of the bond topology data structures
within LAMMPS.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`reset_atom_ids <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
:doc:`fix bond/create <fix_bond_create>`,
:doc:`fix bond/break <fix_bond_break>`,
:doc:`fix evaporate <fix_evaporate>`,
:doc:`delete_atoms <delete_atoms>`,
:doc:`compute fragment/atom <compute_cluster_atom>`
Default
"""""""
The default keyword settings are compress = yes, single = no, and
offset = -1.

11
doc/utils/check-styles.py
View File

@ -52,6 +52,7 @@ minimize = {}
pair = {}
reader = {}
region = {}
total = 0
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
@ -60,7 +61,7 @@ kokkos = re.compile("(.+)/kk$")
kokkos_skip = re.compile("(.+)/kk/(host|device)$")
omp = re.compile("(.+)/omp$")
opt = re.compile("(.+)/opt$")
removed = re.compile("(.+)Deprecated$")
removed = re.compile("(.*)Deprecated$")
def register_style(list,style,info):
if style in list.keys():
@ -119,6 +120,7 @@ for h in headers:
# skip over internal styles w/o explicit documentation
style = m[1]
total += 1
if upper.match(style):
continue
@ -197,12 +199,13 @@ print("""Parsed style names w/o suffixes from C++ tree in %s:
Fix styles: %3d Improper styles: %3d
Integrate styles: %3d Kspace styles: %3d
Minimize styles: %3d Pair styles: %3d
Reader styles: %3d Region styles: %3d""" \
Reader styles: %3d Region styles: %3d
----------------------------------------------------
Total number of styles (including suffixes): %d""" \
% (src, len(angle), len(atom), len(body), len(bond), \
len(command), len(compute), len(dihedral), len(dump), \
len(fix), len(improper), len(integrate), len(kspace), \
len(minimize), len(pair), len(reader), len(region)))
len(minimize), len(pair), len(reader), len(region), total))
counter = 0

1
doc/utils/sphinx-config/false_positives.txt
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@ -2058,6 +2058,7 @@ nodeless
nodeset
nodesets
Noehring
Noffset
noforce
Noid
nolib

1
examples/threebody/CdTeZnSeHgS0.sw Symbolic link
View File

@ -0,0 +1 @@
../../potentials/CdTeZnSeHgS0.sw

6
python/lammps.py
View File

@ -204,6 +204,12 @@ class lammps(object):
self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.restype = None
self.lib.lammps_has_error.argtypes = [c_void_p]
self.lib.lammps_has_error.restype = c_bool
self.lib.lammps_get_last_error_message.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_get_last_error_message.restype = c_int
# if no ptr provided, create an instance of LAMMPS
# don't know how to pass an MPI communicator from PyPar
# but we can pass an MPI communicator from mpi4py v2.0.0 and later

3
src/angle_deprecated.cpp
View File

@ -44,8 +44,7 @@ void AngleDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nAngle style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This angle style is no longer available");
error->all(FLERR,"This angle style is no longer available");
}

3
src/bond_deprecated.cpp
View File

@ -44,8 +44,7 @@ void BondDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nBond style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This bond style is no longer available");
error->all(FLERR,"This bond style is no longer available");
}

3
src/compute_deprecated.cpp
View File

@ -31,6 +31,5 @@ ComputeDeprecated::ComputeDeprecated(LAMMPS *lmp, int narg, char **arg) :
utils::logmesg(lmp,"\nCompute style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This compute style is no longer available");
error->all(FLERR,"This compute style is no longer available");
}

192
src/compute_fragment_atom.cpp
View File

@ -23,37 +23,56 @@
#include "update.h"
#include "modify.h"
#include "force.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
ComputeFragmentAtom::ComputeFragmentAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
fragmentID(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal compute fragment/atom command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute fragment/atom used when bonds are not allowed");
peratom_flag = 1;
size_peratom_cols = 0;
comm_forward = 1;
comm_reverse = 1;
// process optional args
singleflag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"single") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute fragment/atom command");
if (strcmp(arg[iarg+1],"yes") == 0) singleflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) singleflag = 0;
else error->all(FLERR,"Illegal compute fragment/atom command");
iarg += 2;
} else error->all(FLERR,"Illegal compute fragment/atom command");
}
nmax = 0;
stack = NULL;
clist = NULL;
markflag = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeFragmentAtom::~ComputeFragmentAtom()
{
memory->destroy(stack);
memory->destroy(clist);
memory->destroy(markflag);
memory->destroy(fragmentID);
}
@ -63,8 +82,8 @@ void ComputeFragmentAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute fragment/atom unless atoms have IDs");
if (force->bond == NULL)
error->all(FLERR,"Compute fragment/atom requires a bond style to be defined");
if (!atom->molecular)
error->all(FLERR,"Compute fragment/atom requires a molecular system");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@ -77,15 +96,24 @@ void ComputeFragmentAtom::init()
void ComputeFragmentAtom::compute_peratom()
{
int i,j,k;
int i,j,k,m,n;
int nstack,ncluster,done,alldone;
double newID,cID;
tagint *list;
invoked_peratom = update->ntimestep;
// grow fragmentID array if necessary
// grow work and fragmentID vectors if necessary
if (atom->nmax > nmax) {
memory->destroy(stack);
memory->destroy(clist);
memory->destroy(markflag);
memory->destroy(fragmentID);
nmax = atom->nmax;
memory->create(stack,nmax,"fragment/atom:stack");
memory->create(clist,nmax,"fragment/atom:clist");
memory->create(markflag,nmax,"fragment/atom:markflag");
memory->create(fragmentID,nmax,"fragment/atom:fragmentID");
vector_atom = fragmentID;
}
@ -97,63 +125,111 @@ void ComputeFragmentAtom::compute_peratom()
comm->forward_comm_compute(this);
}
// each atom starts in its own fragment,
// owned + ghost atoms start with fragmentID = atomID
// atoms not in group have fragmentID = 0
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
int *mask = atom->mask;
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nlocal + atom->nghost; i++)
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) fragmentID[i] = tag[i];
else fragmentID[i] = 0;
}
// loop until no more changes on any proc:
// loop until no ghost atom fragment ID is changed
// acquire fragmentIDs of ghost atoms
// loop over my atoms, and check atoms bound to it
// if both atoms are in fragment, assign lowest fragmentID to both
// iterate until no changes in my atoms
// then check if any proc made changes
// loop over clusters of atoms, which include ghost atoms
// set fragmentIDs for each cluster to min framentID in the clusters
// if singleflag = 0 atoms without bonds are assigned fragmentID = 0
// iterate until no changes to ghost atom fragmentIDs
commflag = 1;
int change,done,anychange;
int iteration = 0;
while (1) {
iteration++;
comm->forward_comm_compute(this);
// reverse communication when bonds are not stored on every processor
if (force->newton_bond)
comm->reverse_comm_compute(this);
change = 0;
while (1) {
done = 1;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
for (j = 0; j < num_bond[i]; j++) {
if (bond_type[i][j] == 0) continue;
k = atom->map(bond_atom[i][j]);
// set markflag = 0 for all owned atoms, for new iteration
for (i = 0; i < nlocal; i++) markflag[i] = 0;
// loop over all owned atoms
// each unmarked atom starts a cluster search
for (i = 0; i < nlocal; i++) {
// skip atom I if not in group or already marked
// if singleflag = 0 and atom has no bond partners, fragID = 0 and done
if (!(mask[i] & groupbit)) continue;
if (markflag[i]) continue;
if (!singleflag && (nspecial[i][0] == 0)) {
fragmentID[i] = 0.0;
continue;
}
// find one cluster of bond-connected atoms
// ncluster = # of owned and ghost atoms in cluster
// clist = vector of local indices of the ncluster atoms
// stack is used to walk the bond topology
ncluster = nstack = 0;
stack[nstack++] = i;
while (nstack) {
j = stack[--nstack];
clist[ncluster++] = j;
markflag[j] = 1;
n = nspecial[j][0];
list = special[j];
for (m = 0; m < n; m++) {
k = atom->map(list[m]);
// skip bond neighbor K if not in group or already marked
if (k < 0) continue;
if (!(mask[k] & groupbit)) continue;
if (fragmentID[i] == fragmentID[k]) continue;
if (k < nlocal && markflag[k]) continue;
fragmentID[i] = fragmentID[k] = MIN(fragmentID[i],fragmentID[k]);
done = 0;
// owned bond neighbors are added to stack for further walking
// ghost bond neighbors are added directly w/out use of stack
if (k < nlocal) stack[nstack++] = k;
else clist[ncluster++] = k;
}
}
if (!done) change = 1;
if (done) break;
// newID = minimum fragment ID in cluster list, including ghost atoms
newID = BIG;
for (m = 0; m < ncluster; m++) {
cID = fragmentID[clist[m]];
newID = MIN(newID,cID);
}
// set fragmentID = newID for all atoms in cluster, including ghost atoms
// not done with iterations if change the fragmentID of a ghost atom
for (m = 0; m < ncluster; m++) {
j = clist[m];
if (j >= nlocal && fragmentID[j] != newID) done = 0;
fragmentID[j] = newID;
}
}
// stop if all procs are done
MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
if (!anychange) break;
MPI_Allreduce(&done,&alldone,1,MPI_INT,MPI_MIN,world);
if (alldone) break;
}
}
@ -203,43 +279,13 @@ void ComputeFragmentAtom::unpack_forward_comm(int n, int first, double *buf)
}
}
/* ---------------------------------------------------------------------- */
int ComputeFragmentAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = fragmentID[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeFragmentAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
double x = buf[m++];
// only overwrite local IDs with values lower than current ones
fragmentID[j] = MIN(x,fragmentID[j]);
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double ComputeFragmentAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
bytes += 3*nmax * sizeof(int);
return bytes;
}

5
src/compute_fragment_atom.h
View File

@ -32,12 +32,11 @@ class ComputeFragmentAtom : public Compute {
void compute_peratom();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
private:
int nmax,commflag;
int nmax,commflag,singleflag;
int *stack,*clist,*markflag;
double *fragmentID;
};

24
src/deprecated.cpp
View File

@ -16,29 +16,27 @@
------------------------------------------------------------------------- */
#include "deprecated.h"
#include <cstring>
#include <string>
#include "comm.h"
#include "error.h"
#include "input.h"
#include "utils.h"
using namespace LAMMPS_NS;
static void writemsg(LAMMPS *lmp, const char *msg, int abend=1)
{
if (lmp->comm->me == 0) {
if (lmp->screen) fputs(msg,lmp->screen);
if (lmp->logfile) fputs(msg,lmp->logfile);
}
if (abend)
lmp->error->all(FLERR,"This command is no longer available");
}
/* ---------------------------------------------------------------------- */
void Deprecated::command(int /* narg */, char ** /* arg */)
{
if (strcmp(input->command,"DEPRECATED") == 0) {
writemsg(lmp,"\nCommand 'DEPRECATED' is a dummy command\n\n",0);
const std::string cmd = input->command;
if (cmd == "DEPRECATED") {
if (lmp->comm->me == 0)
utils::logmesg(lmp,"\nCommand 'DEPRECATED' is a dummy command\n\n");
return;
} else if (cmd == "reset_ids") {
if (lmp->comm->me == 0)
utils::logmesg(lmp,"\n'reset_ids' has been renamed to 'reset_atom_ids'\n\n");
}
error->all(FLERR,"This command is no longer available");
}

1
src/deprecated.h
View File

@ -14,6 +14,7 @@
#ifdef COMMAND_CLASS
CommandStyle(DEPRECATED,Deprecated)
CommandStyle(reset_ids,Deprecated)
#else

3
src/dihedral_deprecated.cpp
View File

@ -45,6 +45,5 @@ void DihedralDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nDihedral style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This dihedral style is no longer available");
error->all(FLERR,"This dihedral style is no longer available");
}

3
src/dump_deprecated.cpp
View File

@ -31,6 +31,5 @@ DumpDeprecated::DumpDeprecated(LAMMPS *lmp, int narg, char **arg) :
utils::logmesg(lmp,"\nDump style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This dump style is no longer available");
error->all(FLERR,"This dump style is no longer available");
}

3
src/fix_deprecated.cpp
View File

@ -43,6 +43,5 @@ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) :
"compute chunk/atom:\n dim, origin, delta, region, "
"bound, discard, units\n\n");
}
lmp->error->all(FLERR,"This fix style is no longer available");
error->all(FLERR,"This fix style is no longer available");
}

3
src/improper_deprecated.cpp
View File

@ -45,8 +45,7 @@ void ImproperDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nImproper style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This improper style is no longer available");
error->all(FLERR,"This improper style is no longer available");
}

2
src/input.cpp
View File

@ -227,7 +227,7 @@ void Input::file()
// execute the command
if (execute_command())
if (execute_command() && line)
error->all(FLERR,fmt::format("Unknown command: {}",line));
}
}

3
src/kspace_deprecated.cpp
View File

@ -35,8 +35,7 @@ void KSpaceDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nKSpace style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This kspace style is no longer available");
error->all(FLERR,"This kspace style is no longer available");
}

3
src/pair_deprecated.cpp
View File

@ -50,6 +50,5 @@ void PairDeprecated::settings(int, char **)
utils::logmesg(lmp,"\nPair style 'reax' has been removed from LAMMPS "
"after the 12 December 2018 version\n\n");
}
lmp->error->all(FLERR,"This pair style is no longer available");
error->all(FLERR,"This pair style is no longer available");
}

2
src/region_deprecated.cpp
View File

@ -31,5 +31,5 @@ RegionDeprecated::RegionDeprecated(LAMMPS *lmp, int narg, char **arg) :
utils::logmesg(lmp,"\nRegion style 'DEPRECATED' is a dummy style\n\n");
return;
}
lmp->error->all(FLERR,"This region style is no longer available");
error->all(FLERR,"This region style is no longer available");
}

32
src/reset_ids.cpp → src/reset_atom_ids.cpp
View File

@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "reset_ids.h"
#include "reset_atom_ids.h"
#include <mpi.h>
#include <cstring>
#include "atom.h"
@ -53,11 +53,11 @@ void ResetIDs::command(int narg, char **arg)
if (domain->box_exist == 0)
error->all(FLERR,"Reset_ids command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use reset_ids unless atoms have IDs");
error->all(FLERR,"Cannot use reset_atom_ids unless atoms have IDs");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->stores_ids)
error->all(FLERR,"Cannot use reset_ids when a fix exists that stores atom IDs");
error->all(FLERR,"Cannot use reset_atom_ids when a fix exists that stores atom IDs");
if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n");
@ -68,12 +68,12 @@ void ResetIDs::command(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_ids command");
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) sortflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) sortflag = 0;
else error->all(FLERR,"Illegal reset_ids command");
else error->all(FLERR,"Illegal reset_atom_ids command");
iarg += 2;
} else error->all(FLERR,"Illegal reset_ids command");
} else error->all(FLERR,"Illegal reset_atom_ids command");
}
// create an atom map if one doesn't exist already
@ -110,7 +110,7 @@ void ResetIDs::command(int narg, char **arg)
int nall = nlocal + atom->nghost;
tagint *oldIDs;
memory->create(oldIDs,nlocal,"reset_ids:oldIDs");
memory->create(oldIDs,nlocal,"reset_atom_ids:oldIDs");
for (int i = 0; i < nlocal; i++) {
oldIDs[i] = tag[i];
@ -129,7 +129,7 @@ void ResetIDs::command(int narg, char **arg)
// forward_comm_array acquires new IDs for ghost atoms
double **newIDs;
memory->create(newIDs,nall,1,"reset_ids:newIDs");
memory->create(newIDs,nall,1,"reset_atom_ids:newIDs");
for (int i = 0; i < nlocal; i++) {
newIDs[i][0] = ubuf(tag[i]).d;
@ -155,7 +155,7 @@ void ResetIDs::command(int narg, char **arg)
for (j = 0; j < num_bond[i]; j++) {
oldID = bond_atom[i][j];
m = atom->map(oldID);
if (m >= 0) bond_atom[i][j] = static_cast<tagint> (newIDs[m][0]);
if (m >= 0) bond_atom[i][j] = (tagint) ubuf(newIDs[m][0]).i;
else badcount++;
}
}
@ -318,6 +318,15 @@ void ResetIDs::sort()
if (dim == 2) mylo[2] = myhi[2] = 0.0;
// must ensure that bounding box volume is > 0.0
for (int i = 0; i < 3; ++i) {
if (mylo[i] == myhi[i]) {
mylo[i] -= 0.5;
myhi[i] += 0.5;
}
}
MPI_Allreduce(mylo,bboxlo,3,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(myhi,bboxhi,3,MPI_DOUBLE,MPI_MAX,world);
@ -332,7 +341,8 @@ void ResetIDs::sort()
// binsize = edge length of a cubic bin
// nbin xyz = bin count in each dimension
bigint nbin_estimate = atom->natoms / PERBIN;
bigint nbin_estimate = atom->natoms / PERBIN + 1;
double vol;
if (dim == 2) vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]);
else vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]) * (bboxhi[2]-bboxlo[2]);
@ -468,7 +478,7 @@ int ResetIDs::sort_bins(int n, char *inbuf,
if (in[i].ibin < binlo || in[i].ibin >= binhi) {
//printf("BAD me %d i %d %d ibin %d binlohi %d %d\n",
// rptr->comm->me,i,n,in[i].ibin,binlo,binhi);
error->one(FLERR,"Bad spatial bin assignment in reset_ids sort");
error->one(FLERR,"Bad spatial bin assignment in reset_atom_ids sort");
}
ibin = in[i].ibin - binlo;
if (head[ibin] < 0) head[ibin] = i;

4
src/reset_ids.h → src/reset_atom_ids.h
View File

@ -13,7 +13,7 @@
#ifdef COMMAND_CLASS
CommandStyle(reset_ids,ResetIDs)
CommandStyle(reset_atom_ids,ResetIDs)
#else
@ -70,7 +70,7 @@ E: Illegal ... command
UNDOCUMENTED
E: Cannot use reset_ids unless atoms have IDs
E: Cannot use reset_atom_ids unless atoms have IDs
UNDOCUMENTED

214
src/reset_mol_ids.cpp Normal file
View File

@ -0,0 +1,214 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Jacob Gissinger (jacob.gissinger@colorado.edu)
------------------------------------------------------------------------- */
#include "reset_mol_ids.h"
#include <mpi.h>
#include <string>
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "group.h"
#include "modify.h"
#include "compute_fragment_atom.h"
#include "compute_chunk_atom.h"
#include "utils.h"
#include "error.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void ResetMolIDs::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Reset_mol_ids command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use reset_mol_ids unless atoms have IDs");
if (atom->molecular != 1)
error->all(FLERR,"Can only use reset_mol_ids on molecular systems");
// process args
if (narg < 1) error->all(FLERR,"Illegal reset_mol_ids command");
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID");
int groupbit = group->bitmask[igroup];
int compressflag = 1;
int singleflag = 0;
tagint offset = -1;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) compressflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compressflag = 0;
else error->all(FLERR,"Illegal reset_mol_ids command");
iarg += 2;
} else if (strcmp(arg[iarg],"single") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) singleflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) singleflag = 0;
else error->all(FLERR,"Illegal reset_mol_ids command");
iarg += 2;
} else if (strcmp(arg[iarg],"offset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
offset = utils::tnumeric(FLERR,arg[iarg+1],1,lmp);
if (offset < -1) error->all(FLERR,"Illegal reset_mol_ids command");
iarg += 2;
} else error->all(FLERR,"Illegal reset_mol_ids command");
}
if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n");
// record wall time for resetting molecule IDs
MPI_Barrier(world);
double time1 = MPI_Wtime();
// create instances of compute fragment/atom, compute reduce (if needed),
// and compute chunk/atom. all use the group-ID for this command
const std::string idfrag = "reset_mol_ids_FRAGMENT_ATOM";
if (singleflag)
modify->add_compute(fmt::format("{} {} fragment/atom single yes",idfrag,arg[0]));
else
modify->add_compute(fmt::format("{} {} fragment/atom single no",idfrag,arg[0]));
const std::string idchunk = "reset_mol_ids_CHUNK_ATOM";
if (compressflag)
modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes",
idchunk,arg[0]));
// initialize system since comm->borders() will be invoked
lmp->init();
// setup domain, communication
// exchange will clear map, borders will reset
// this is the map needed to lookup current global IDs for bond topology
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
// invoke peratom method of compute fragment/atom
// walks bond connectivity and assigns each atom a fragment ID
// if singleflag = 0, atoms w/out bonds will be assigned fragID = 0
int icompute = modify->find_compute(idfrag);
ComputeFragmentAtom *cfa = (ComputeFragmentAtom *) modify->compute[icompute];
cfa->compute_peratom();
double *fragIDs = cfa->vector_atom;
// copy fragID to molecule ID for atoms in group
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
molecule[i] = static_cast<tagint> (fragIDs[i]);
// if compressflag = 0, done
// set nchunk = -1 since cannot easily determine # of new molecule IDs
int nchunk = -1;
// if compressflag = 1, invoke peratom method of compute chunk/atom
// will compress new molecule IDs to be contiguous 1 to Nmol
// NOTE: use of compute chunk/atom limits Nmol to a 32-bit int
if (compressflag) {
icompute = modify->find_compute(idchunk);
ComputeChunkAtom *cca = (ComputeChunkAtom *) modify->compute[icompute];
cca->compute_peratom();
double *chunkIDs = cca->vector_atom;
nchunk = cca->nchunk;
// if singleflag = 0, check if any single (no-bond) atoms exist
// if so, they have fragID = 0, and compression just set their chunkID = 1
// singleexist = 0/1 if no/yes single atoms exist with chunkID = 1
int singleexist = 0;
if (!singleflag) {
int mysingle = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (fragIDs[i] == 0.0) mysingle = 1;
MPI_Allreduce(&mysingle,&singleexist,1,MPI_INT,MPI_MAX,world);
if (singleexist) nchunk--;
}
// if offset < 0 (default), reset it
// if group = all, offset = 0
// else offset = largest molID of non-group atoms
if (offset < 0) {
if (groupbit != 1) {
tagint mymol = 0;
for (int i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit))
mymol = MAX(mymol,molecule[i]);
MPI_Allreduce(&mymol,&offset,1,MPI_LMP_TAGINT,MPI_MAX,world);
} else offset = 0;
}
// reset molecule ID for all atoms in group
// newID = chunkID + offset
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
tagint newid = static_cast<tagint>(chunkIDs[i]);
if (singleexist) {
if (newid == 1) newid = 0;
else newid += offset - 1;
} else newid += offset;
molecule[i] = newid;
}
}
}
// clean up
modify->delete_compute(idfrag);
if (compressflag) modify->delete_compute(idchunk);
// total time
MPI_Barrier(world);
if (comm->me == 0) {
if (nchunk < 0)
utils::logmesg(lmp,fmt::format(" number of new molecule IDs = unknown\n"));
else
utils::logmesg(lmp,fmt::format(" number of new molecule IDs = {}\n",nchunk));
utils::logmesg(lmp,fmt::format(" reset_mol_ids CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}
}

60
src/reset_mol_ids.h Normal file
View File

@ -0,0 +1,60 @@
/* -*- 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 COMMAND_CLASS
CommandStyle(reset_mol_ids,ResetMolIDs)
#else
#ifndef LMP_RESET_MOL_IDS_H
#define LMP_RESET_MOL_IDS_H
#include "pointers.h"
namespace LAMMPS_NS {
class ResetMolIDs : protected Pointers {
public:
ResetMolIDs(class LAMMPS *);
void command(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Reset_mol_ids command before simulation box is defined
UNDOCUMENTED
E: Can only use reset_mol_ids on molecular systems
UNDOCUMENTED
E: Illegal ... command
UNDOCUMENTED
E: Cannot use reset_mol_ids unless molecules have IDs
UNDOCUMENTED
E: Reset_mol_ids missing %d bond topology atom IDs - use comm_modify cutoff
UNDOCUMENTED
*/

5
unittest/commands/CMakeLists.txt
View File

@ -2,3 +2,8 @@
add_executable(test_simple_commands test_simple_commands.cpp)
target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME SimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_reset_ids test_reset_ids.cpp)
target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME ResetIDs COMMAND test_reset_ids WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

1
unittest/commands/data.fourmol Symbolic link
View File

@ -0,0 +1 @@
../force-styles/tests/data.fourmol

1
unittest/commands/in.fourmol Symbolic link
View File

@ -0,0 +1 @@
../force-styles/tests/in.fourmol

562
unittest/commands/test_reset_ids.cpp Normal file
View File

@ -0,0 +1,562 @@
/* ----------------------------------------------------------------------
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 "atom.h"
#include "fmt/format.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "output.h"
#include "update.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
using LAMMPS_NS::utils::split_words;
namespace LAMMPS_NS {
using ::testing::MatchesRegex;
#define GETIDX(i) lmp->atom->map(i)
#define TEST_FAILURE(...) \
if (Info::has_exceptions()) { \
ASSERT_ANY_THROW({__VA_ARGS__}); \
} else { \
ASSERT_DEATH({__VA_ARGS__}, ""); \
}
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
class ResetIDsTest : public ::testing::Test {
protected:
LAMMPS *lmp;
void SetUp() override
{
const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
Info *info = new Info(lmp);
if (info->has_style("atom", "full")) {
lmp->input->one("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER));
lmp->input->one("include ${input_dir}/in.fourmol");
}
delete info;
if (!verbose) ::testing::internal::GetCapturedStdout();
}
void TearDown() override
{
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
}
};
TEST_F(ResetIDsTest, MolIDAll)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 3);
ASSERT_EQ(molid[GETIDX(19)], 3);
ASSERT_EQ(molid[GETIDX(20)], 3);
ASSERT_EQ(molid[GETIDX(21)], 4);
ASSERT_EQ(molid[GETIDX(22)], 4);
ASSERT_EQ(molid[GETIDX(23)], 4);
ASSERT_EQ(molid[GETIDX(24)], 5);
ASSERT_EQ(molid[GETIDX(25)], 5);
ASSERT_EQ(molid[GETIDX(26)], 5);
ASSERT_EQ(molid[GETIDX(27)], 6);
ASSERT_EQ(molid[GETIDX(28)], 6);
ASSERT_EQ(molid[GETIDX(29)], 6);
// the original data file has two different molecule IDs
// for two residues of the same molecule/fragment.
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 4);
ASSERT_EQ(molid[GETIDX(26)], 4);
ASSERT_EQ(molid[GETIDX(27)], 5);
ASSERT_EQ(molid[GETIDX(28)], 5);
ASSERT_EQ(molid[GETIDX(29)], 5);
}
TEST_F(ResetIDsTest, DeletePlusAtomID)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group twowater molecule 4:6:2");
lmp->input->one("delete_atoms group twowater compress no bond yes");
lmp->input->one("reset_mol_ids all");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(24)], 3);
ASSERT_EQ(molid[GETIDX(25)], 3);
ASSERT_EQ(molid[GETIDX(26)], 3);
// now also check and reset the atom ids
ASSERT_GE(GETIDX(1), 0);
ASSERT_GE(GETIDX(2), 0);
ASSERT_GE(GETIDX(3), 0);
ASSERT_GE(GETIDX(4), 0);
ASSERT_GE(GETIDX(5), 0);
ASSERT_GE(GETIDX(6), 0);
ASSERT_GE(GETIDX(7), 0);
ASSERT_GE(GETIDX(8), 0);
ASSERT_GE(GETIDX(9), 0);
ASSERT_GE(GETIDX(10), 0);
ASSERT_GE(GETIDX(11), 0);
ASSERT_GE(GETIDX(12), 0);
ASSERT_GE(GETIDX(13), 0);
ASSERT_GE(GETIDX(14), 0);
ASSERT_GE(GETIDX(15), 0);
ASSERT_GE(GETIDX(16), 0);
ASSERT_GE(GETIDX(17), 0);
ASSERT_GE(GETIDX(18), 0);
ASSERT_GE(GETIDX(19), 0);
ASSERT_GE(GETIDX(20), 0);
ASSERT_EQ(GETIDX(21), -1);
ASSERT_EQ(GETIDX(22), -1);
ASSERT_EQ(GETIDX(23), -1);
ASSERT_GE(GETIDX(24), 0);
ASSERT_GE(GETIDX(25), 0);
ASSERT_GE(GETIDX(26), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_atom_ids");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
for (int i = 1; i <= 23; ++i)
ASSERT_GE(GETIDX(i), 0);
}
TEST_F(ResetIDsTest, PartialOffset)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group nowater subtract all allwater");
lmp->input->one("reset_mol_ids allwater offset 4");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 29);
ASSERT_EQ(lmp->atom->map_tag_max, 29);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 5);
ASSERT_EQ(molid[GETIDX(19)], 5);
ASSERT_EQ(molid[GETIDX(20)], 5);
ASSERT_EQ(molid[GETIDX(21)], 6);
ASSERT_EQ(molid[GETIDX(22)], 6);
ASSERT_EQ(molid[GETIDX(23)], 6);
ASSERT_EQ(molid[GETIDX(24)], 7);
ASSERT_EQ(molid[GETIDX(25)], 7);
ASSERT_EQ(molid[GETIDX(26)], 7);
ASSERT_EQ(molid[GETIDX(27)], 8);
ASSERT_EQ(molid[GETIDX(28)], 8);
ASSERT_EQ(molid[GETIDX(29)], 8);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids nowater offset 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 5);
ASSERT_EQ(molid[GETIDX(19)], 5);
ASSERT_EQ(molid[GETIDX(20)], 5);
ASSERT_EQ(molid[GETIDX(21)], 6);
ASSERT_EQ(molid[GETIDX(22)], 6);
ASSERT_EQ(molid[GETIDX(23)], 6);
ASSERT_EQ(molid[GETIDX(24)], 7);
ASSERT_EQ(molid[GETIDX(25)], 7);
ASSERT_EQ(molid[GETIDX(26)], 7);
ASSERT_EQ(molid[GETIDX(27)], 8);
ASSERT_EQ(molid[GETIDX(28)], 8);
ASSERT_EQ(molid[GETIDX(29)], 8);
}
TEST_F(ResetIDsTest, DeleteAdd)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group twowater molecule 4:6:2");
lmp->input->one("group nowater subtract all allwater");
lmp->input->one("delete_atoms group twowater compress no bond yes mol yes");
lmp->input->one("reset_mol_ids allwater");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 3);
ASSERT_EQ(molid[GETIDX(19)], 3);
ASSERT_EQ(molid[GETIDX(20)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 4);
ASSERT_EQ(molid[GETIDX(26)], 4);
// now also check and reset the atom ids
ASSERT_GE(GETIDX(1), 0);
ASSERT_GE(GETIDX(2), 0);
ASSERT_GE(GETIDX(3), 0);
ASSERT_GE(GETIDX(4), 0);
ASSERT_GE(GETIDX(5), 0);
ASSERT_GE(GETIDX(6), 0);
ASSERT_GE(GETIDX(7), 0);
ASSERT_GE(GETIDX(8), 0);
ASSERT_GE(GETIDX(9), 0);
ASSERT_GE(GETIDX(10), 0);
ASSERT_GE(GETIDX(11), 0);
ASSERT_GE(GETIDX(12), 0);
ASSERT_GE(GETIDX(13), 0);
ASSERT_GE(GETIDX(14), 0);
ASSERT_GE(GETIDX(15), 0);
ASSERT_GE(GETIDX(16), 0);
ASSERT_GE(GETIDX(17), 0);
ASSERT_GE(GETIDX(18), 0);
ASSERT_GE(GETIDX(19), 0);
ASSERT_GE(GETIDX(20), 0);
ASSERT_EQ(GETIDX(21), -1);
ASSERT_EQ(GETIDX(22), -1);
ASSERT_EQ(GETIDX(23), -1);
ASSERT_GE(GETIDX(24), 0);
ASSERT_GE(GETIDX(25), 0);
ASSERT_GE(GETIDX(26), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_atom_ids sort yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
for (int i = 1; i <= 23; ++i)
ASSERT_GE(GETIDX(i), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids nowater offset 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 2);
ASSERT_EQ(molid[GETIDX(2)], 2);
ASSERT_EQ(molid[GETIDX(3)], 2);
ASSERT_EQ(molid[GETIDX(4)], 2);
ASSERT_EQ(molid[GETIDX(5)], 2);
ASSERT_EQ(molid[GETIDX(6)], 2);
ASSERT_EQ(molid[GETIDX(7)], 2);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 3);
ASSERT_EQ(molid[GETIDX(14)], 3);
ASSERT_EQ(molid[GETIDX(15)], 3);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(21)], 4);
ASSERT_EQ(molid[GETIDX(22)], 4);
ASSERT_EQ(molid[GETIDX(23)], 4);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("create_atoms 1 single 0.0 0.0 0.0");
lmp->input->one("create_atoms 2 single 1.0 0.0 0.0");
lmp->input->one("create_atoms 3 single 2.0 0.0 0.0");
lmp->input->one("create_atoms 4 single 3.0 0.0 0.0");
lmp->input->one("reset_mol_ids all single yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 27);
ASSERT_EQ(lmp->atom->map_tag_max, 27);
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 5);
ASSERT_EQ(molid[GETIDX(26)], 6);
ASSERT_EQ(molid[GETIDX(27)], 7);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all single no");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 0);
ASSERT_EQ(molid[GETIDX(25)], 0);
ASSERT_EQ(molid[GETIDX(26)], 0);
ASSERT_EQ(molid[GETIDX(27)], 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all compress no single yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(21)], 21);
ASSERT_EQ(molid[GETIDX(22)], 21);
ASSERT_EQ(molid[GETIDX(23)], 21);
ASSERT_EQ(molid[GETIDX(24)], 24);
ASSERT_EQ(molid[GETIDX(25)], 25);
ASSERT_EQ(molid[GETIDX(26)], 26);
ASSERT_EQ(molid[GETIDX(27)], 27);
}
TEST_F(ResetIDsTest, DeathTests)
{
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids"););
auto mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset 1 1"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset -2"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR on proc 0: Expected integer.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress yes single no offset xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR on proc 0: Expected integer.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all single"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all single xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
}
TEST(ResetMolIds, CMDFail)
{
LAMMPS *lmp;
const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
if (!verbose) ::testing::internal::GetCapturedStdout();
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
auto mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Reset_mol_ids command before.*"));
::testing::internal::CaptureStdout();
lmp->input->one("atom_modify id no");
lmp->input->one("region box block 0 1 0 1 0 1");
lmp->input->one("create_box 1 box");
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Cannot use reset_mol_ids unl.*"));
::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("region box block 0 1 0 1 0 1");
lmp->input->one("create_box 1 box");
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Can only use reset_mol_ids.*"));
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
};
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}

6
unittest/formats/test_atom_styles.cpp
View File

@ -423,7 +423,7 @@ TEST_F(AtomStyleTest, atomic)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 3);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_ids");
lmp->input->one("reset_atom_ids");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 2);
ASSERT_EQ(lmp->atom->tag_consecutive(), 1);
@ -810,7 +810,7 @@ TEST_F(AtomStyleTest, charge)
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_ids");
lmp->input->one("reset_atom_ids");
lmp->input->one("replicate 2 2 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 16);
@ -1137,7 +1137,7 @@ TEST_F(AtomStyleTest, sphere)
EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
lmp->input->one("read_restart test_atom_styles.restart");
lmp->input->one("replicate 1 1 2");
lmp->input->one("reset_ids");
lmp->input->one("reset_atom_ids");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("sphere"));
ASSERT_NE(lmp->atom->avec, nullptr);