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Merge remote-tracking branch 'github/develop' into general-triclinic

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This commit is contained in:
Axel Kohlmeyer
2024-04-02 09:41:21 -04:00
parent 1bdcf7e42e a017a775bd
commit ed0cff92de
37 changed files with 457 additions and 373 deletions
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7
cmake/Modules/Packages/KOKKOS.cmake
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@ -139,12 +139,9 @@ if(PKG_KSPACE)
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_library(CUFFT_LIBRARY cufft)
if (CUFFT_LIBRARY STREQUAL "CUFFT_LIBRARY-NOTFOUND")
message(FATAL_ERROR "Required cuFFT library not found. Check your environment or set CUFFT_LIBRARY to its location")
endif()
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE ${CUFFT_LIBRARY})
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))

4
doc/src/Fortran.rst
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@ -1255,8 +1255,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
three elements of the global vector calculated by fix recenter into the
variables *dx*, *dy*, and *dz*, respectively.
If asked for per-atom or local data, :f:func:`extract_compute` returns a
pointer to actual LAMMPS data. The pointer so returned will have the
If asked for per-atom or local data, :f:func:`extract_fix` returns a
pointer to actual LAMMPS data. The pointer returned will have the
appropriate size to match the internal data, and will be
type/kind/rank-checked at the time of the assignment. For example,

28
doc/src/fix_ave_chunk.rst
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@ -31,7 +31,7 @@ Syntax
v_name = per-atom vector calculated by an atom-style variable with name
* zero or more keyword/arg pairs may be appended
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *append* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -51,6 +51,8 @@ Syntax
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
*file* arg = filename
filename = file to write results to
*append* arg = filename
filename = file to append results to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -433,15 +435,21 @@ molecule.
----------
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
text file in the following format. A line with the timestep and number of
chunks is written. Then one line per chunk is written, containing the chunk
ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of atoms
in the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every :math:`N_\text{freq}`
timesteps, a section of chunk info will be written to a text file in the
following format. A line with the timestep and number of chunks is
written. Then one line per chunk is written, containing the chunk ID
:math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of
atoms in the chunk, and one or more calculated values. More explanation
of the optional values is given below. The number of values in each
line corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
quantities, as explained above.

36
doc/src/fix_ave_histo.rst
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@ -35,7 +35,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
* keyword = *mode* or *kind* or *file* or *append* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
*kind* arg = *global* or *peratom* or *local*
*file* arg = filename
filename = name of file to output histogram(s) to
*append* arg = filename
filename = name of file to append histogram(s) to
*ave* args = *one* or *running* or *window*
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
@ -317,19 +319,25 @@ on. The default is step 0. Often input values can be 0.0 at time 0,
so setting *start* to a larger value can avoid including a 0.0 in
a running or windowed histogram.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one histogram is written to the file. This includes a leading
line that contains the timestep, number of bins, the total count of
values contributing to the histogram, the count of values that were
not histogrammed (see the *beyond* keyword), the minimum value
encountered, and the maximum value encountered. The min/max values
include values that were not histogrammed. Following the leading
line, one line per bin is written into the file. Each line contains
the bin #, the coordinate for the center of the bin (between *lo* and
*hi*\ ), the count of values in the bin, and the normalized count. The
normalized count is the bin count divided by the total count (not
including values not histogrammed), so that the normalized values sum
to 1.0 across all bins.
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
histogram is written to the file. This includes a leading line that
contains the timestep, number of bins, the total count of values
contributing to the histogram, the count of values that were not
histogrammed (see the *beyond* keyword), the minimum value encountered,
and the maximum value encountered. The min/max values include values
that were not histogrammed. Following the leading line, one line per
bin is written into the file. Each line contains the bin #, the
coordinate for the center of the bin (between *lo* and *hi*\ ), the
count of values in the bin, and the normalized count. The normalized
count is the bin count divided by the total count (not including values
not histogrammed), so that the normalized values sum to 1.0 across all
bins.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of

29
doc/src/fix_ave_time.rst
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@ -28,7 +28,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *mode* or *file* or *append* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
M = value # from 1 to Nvalues
*file* arg = filename
filename = name of file to output time averages to
*append* arg = filename
filename = name of file to append time averages to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -270,16 +272,21 @@ are effectively constant or are simply current values (e.g., they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output).
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For *mode* =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For *mode* = vector, an array
of numbers is written each time output is performed. The number of rows
is the length of the input vectors, and the number of columns is the
number of values. Thus the file ends up to be a series of these array
sections.
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
quantity or vector of quantities is written to the file for each input
value specified in the fix ave/time command. For *mode* = scalar, this
means a single line is written each time output is performed. Thus the
file ends up to be a series of lines, i.e. one column of numbers for
each input value. For *mode* = vector, an array of numbers is written
each time output is performed. The number of rows is the length of the
input vectors, and the number of columns is the number of values. Thus
the file ends up to be a series of these array sections.
.. versionadded:: 4May2022

29
doc/src/fix_electrode.rst
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@ -255,23 +255,24 @@ and the fix will issue an error in that case.
.. versionadded:: TBD
The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
to add an overall potential to all electrodes so that the total charge on
the electrodes is a specified amount (which may be an equal-style variable).
For example, if a user wanted to simulate a solution of excess cations
such that the total electrolyte charge is +2, setting *qtotal -2* would cause
the total electrode charge to be -2, so that the simulation box remains overall
electroneutral. Since *fix electrode/conq* constrains the total charges of
individual electrodes, and since *symm on* constrains the total charge of all
electrodes to be zero, either option is incompatible with the *qtotal* keyword
(even if *qtotal* is set to zero).
The keyword *qtotal* causes *fix electrode/conp* and *fix
electrode/thermo* to add an overall potential to all electrodes so that
the total charge on the electrodes is a specified amount (which may be
an equal-style variable). For example, if a user wanted to simulate a
solution of excess cations such that the total electrolyte charge is +2,
setting *qtotal -2* would cause the total electrode charge to be -2, so
that the simulation box remains overall electroneutral. Since *fix
electrode/conq* constrains the total charges of individual electrodes,
and since *symm on* constrains the total charge of all electrodes to be
zero, either option is incompatible with the *qtotal* keyword (even if
*qtotal* is set to zero).
.. versionadded:: TBD
The keyword *eta* takes the name of a custom double vector defined via fix
property/atom. The values will be used instead of the standard eta value. The
property/atom fix must be for vector of double values and use the *ghost on*
option.
The keyword *eta* takes the name of a custom double vector defined via
fix property/atom. The values will be used instead of the standard eta
value. The property/atom fix must be for vector of double values and
use the *ghost on* option.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

26
doc/src/processors.rst
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@ -159,17 +159,17 @@ surface-to-volume ratio of each processor's subdomain.
for most MPI implementations, but some MPIs provide options for this
ordering, e.g. via environment variable settings.
The *numa* style operates similar to the *twolevel* keyword except
that it auto-detects which cores are running on which nodes.
It will also subdivide the cores into numa domains. Currently, the
number of numa domains is not autodetected and must be specified using
the *numa_nodes* keyword; otherwise, the default value is used. The
*numa* style uses a different algorithm than the *twolevel* keyword for
doing the two-level factorization of the simulation box into a 3d
processor grid to minimize off-node communication and communication
across numa domains. It does its own MPI-based mapping of nodes and
cores to the regular 3d grid. Thus it may produce a different layout
of the processors than the *twolevel* options.
The *numa* style operates similar to the *twolevel* keyword except that
it auto-detects which cores are running on which nodes. It will also
subdivide the cores into numa domains. Currently, the number of numa
domains is not auto-detected and must be specified using the
*numa_nodes* keyword; otherwise, the default value is used. The *numa*
style uses a different algorithm than the *twolevel* keyword for doing
the two-level factorization of the simulation box into a 3d processor
grid to minimize off-node communication and communication across numa
domains. It does its own MPI-based mapping of nodes and cores to the
regular 3d grid. Thus it may produce a different layout of the
processors than the *twolevel* options.
The *numa* style will give an error if the number of MPI processes is
not divisible by the number of cores used per node, or any of the Px
@ -182,7 +182,7 @@ or Py or Pz values is greater than 1.
is because it auto-detects which processes are running on which nodes.
However, it assumes that the lowest ranks are in the first numa
domain, and so forth. MPI rank orderings that do not preserve this
property might result in more intranode communication between CPUs.
property might result in more intra-node communication between CPUs.
The *custom* style uses the file *infile* to define both the 3d
factorization and the mapping of processors to the grid.
@ -213,7 +213,7 @@ any order, but no processor ID should appear more than once.
----------
The *numa_nodes* keyword is used to specifiy the number of numa domains
The *numa_nodes* keyword is used to specify the number of numa domains
per node. It is currently only used by the *numa* style for two-level
factorization to reduce the amount of MPI communications between CPUs.
A good setting for this will typically be equal to the number of CPU

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -960,6 +960,7 @@ elastance
Electroneg
electronegative
electronegativity
electroneutral
electroneutrality
Eleftheriou
ElementN

2
fortran/lammps.f90
View File

@ -3687,7 +3687,7 @@ CONTAINS
n = LEN_TRIM(f_string)
ptr = lammps_malloc(n+1)
CALL C_F_POINTER(ptr, c_string, [1])
CALL C_F_POINTER(ptr, c_string, [n+1])
DO i=1, n
c_string(i) = f_string(i:i)
END DO

22
lib/gpu/lal_sph_heatconduction.cu
View File

@ -29,23 +29,23 @@ _texture_2d( vel_tex,int4);
#if (SHUFFLE_AVAIL == 0)
#define store_dE(dEacc, ii, inum, tid, t_per_atom, offset, dE) \
#define store_dE(dEacc, ii, inum, tid, t_per_atom, offset, i, dE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add1(t_per_atom, red_acc, offset, tid, dEacc); \
} \
if (offset==0 && ii<inum) { \
dE[ii]=dEacc; \
dE[i]=dEacc; \
}
#else
#define store_drhoE(dEacc, ii, inum, tid, t_per_atom, offset, dE) \
#define store_drhoE(dEacc, ii, inum, tid, t_per_atom, offset, i, dE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
dEacc += shfl_down(dEacc, s, t_per_atom); \
} \
} \
if (offset==0 && ii<inum) { \
dE[ii]=dEacc; \
dE[i]=dEacc; \
}
#endif
@ -66,7 +66,7 @@ __kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
@ -77,7 +77,7 @@ __kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
acctyp dEacc = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -140,7 +140,7 @@ __kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
} // for nbor
} // if ii
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,dE);
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,i,dE);
}
__kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
@ -157,7 +157,7 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
@ -180,7 +180,7 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
acctyp dEacc = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -204,7 +204,7 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype = jx.w;
int jtype=jx.w;
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=coeff[mtype].z;
@ -252,6 +252,6 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
} // for nbor
} // if ii
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,dE);
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,i,dE);
}

45
lib/gpu/lal_sph_lj.cu
View File

@ -29,17 +29,18 @@ _texture_2d( vel_tex,int4);
#if (SHUFFLE_AVAIL == 0)
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, i, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[i]=drhoEacc.x; \
drhoE[i+inum]=drhoEacc.y; \
}
#else
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, i, drhoE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \
@ -47,7 +48,8 @@ _texture_2d( vel_tex,int4);
} \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
drhoE[i]=drhoEacc.x; \
drhoE[i+inum]=drhoEacc.y; \
}
#endif
@ -105,12 +107,12 @@ __kernel void k_sph_lj(const __global numtyp4 *restrict x_,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
__global acctyp *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
@ -124,10 +126,10 @@ __kernel void k_sph_lj(const __global numtyp4 *restrict x_,
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
drhoEacc.x = drhoEacc.y = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -246,7 +248,7 @@ __kernel void k_sph_lj(const __global numtyp4 *restrict x_,
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,i,drhoE);
}
__kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
@ -258,12 +260,12 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
__global acctyp *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
@ -289,10 +291,10 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
drhoEacc.x = drhoEacc.y = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -325,7 +327,7 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype = jx.w;
int jtype=jx.w;
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=coeff[mtype].z; // cutsq[itype][jtype];
@ -415,12 +417,11 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,i,drhoE);
}

64
lib/gpu/lal_sph_taitwater.cu
View File

@ -29,17 +29,18 @@ _texture_2d( vel_tex,int4);
#if (SHUFFLE_AVAIL == 0)
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, i, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[i]=drhoEacc.x; \
drhoE[i+inum]=drhoEacc.y; \
}
#else
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, i, drhoE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \
@ -47,7 +48,8 @@ _texture_2d( vel_tex,int4);
} \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
drhoE[i]=drhoEacc.x; \
drhoE[i+inum]=drhoEacc.y; \
}
#endif
@ -61,12 +63,12 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
__global acctyp *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
@ -80,10 +82,10 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
drhoEacc.x = drhoEacc.y = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -163,9 +165,8 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (soundspeed_itype
+ soundspeed_jtype) * mu / (rhoi + rhoj);
}
fvisc = -coeffx * (soundspeed_itype + soundspeed_jtype) * mu / (rhoi + rhoj);
}
// total pair force & thermal energy increment
numtyp force = -mass_itype * mass_jtype * (fi + fj + fvisc) * wfd;
@ -176,15 +177,11 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
f.z+=delz*force;
// and change in density, drho[i]
drhoEacc.x += mass_jtype* delVdotDelR * wfd;
drhoEacc.x += mass_jtype * delVdotDelR * wfd;
// change in thermal energy, desph[i]
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
@ -198,7 +195,7 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,i,drhoE);
}
__kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
@ -210,12 +207,12 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
__global acctyp *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
@ -245,10 +242,10 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
drhoEacc.x = drhoEacc.y = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
@ -337,8 +334,7 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (soundspeed_itype
+ soundspeed_jtype) * mu / (rhoi + rhoj);
fvisc = -coeffx * (soundspeed_itype + soundspeed_jtype) * mu / (rhoi + rhoj);
}
// total pair force & thermal energy increment
@ -349,16 +345,12 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
f.y+=dely*force;
f.z+=delz*force;
// and change in density
// and change in density, drho[i]
drhoEacc.x += mass_jtype * delVdotDelR * wfd;
// change in thermal energy
// change in thermal energy, desph[i]
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
@ -372,6 +364,6 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,i,drhoE);
}

26
python/lammps/core.py
View File

@ -1078,15 +1078,23 @@ class lammps(object):
def extract_fix(self,fid,fstyle,ftype,nrow=0,ncol=0):
"""Retrieve data from a LAMMPS fix
This is a wrapper around the :cpp:func:`lammps_extract_fix`
function of the C-library interface.
This function returns ``None`` if either the fix id is not
recognized, or an invalid combination of :ref:`fstyle <py_style_constants>`
and :ref:`ftype <py_type_constants>` constants is used. The
names and functionality of the constants are the same as for
the corresponding C-library function. For requests to return
a scalar or a size, the value is returned, also when accessing
global vectors or arrays, otherwise a pointer.
This is a wrapper around the :cpp:func:`lammps_extract_fix` function
of the C-library interface. This function returns ``None`` if
either the fix id is not recognized, or an invalid combination of
:ref:`fstyle <py_style_constants>` and :ref:`ftype
<py_type_constants>` constants is used. The names and functionality
of the constants are the same as for the corresponding C-library
function. For requests to return a scalar or a size, the value is
returned, also when accessing global vectors or arrays, otherwise a
pointer.
.. note::
When requesting global data, the fix data can only be accessed
one item at a time without access to the whole vector or array.
Thus this function will always return a scalar. To access vector
or array elements the "nrow" and "ncol" arguments need to be set
accordingly (they default to 0).
:param fid: fix ID
:type fid: string

7
python/lammps/numpy_wrapper.py
View File

@ -203,6 +203,13 @@ class numpy_wrapper:
It behaves the same as the original method, but returns NumPy arrays
instead of ``ctypes`` pointers.
.. note::
When requesting global data, the fix data can only be accessed one
item at a time without access to the whole vector or array. Thus this
function will always return a scalar. To access vector or array elements
the "nrow" and "ncol" arguments need to be set accordingly (they default to 0).
:param fid: fix ID
:type fid: string
:param fstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`

18
src/EFF/fix_nh_eff.cpp
View File

@ -16,7 +16,6 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include "fix_nh_eff.h"
#include "atom.h"
@ -62,7 +61,7 @@ void FixNHEff::nve_v()
if (mask[i] & groupbit) {
if (abs(spin[i])==1) {
dtfm = dtf / mass[type[i]];
ervel[i] = dtfm * erforce[i] / mefactor;
ervel[i] += dtfm * erforce[i] / mefactor;
}
}
}
@ -79,15 +78,26 @@ void FixNHEff::nve_x()
FixNH::nve_x();
double *eradius = atom->eradius;
double *erforce = atom->erforce;
double *ervel = atom->ervel;
double *mass = atom->mass;
int *type = atom->type;
int *spin = atom->spin;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double mefactor = domain->dimension/4.0;
double dtfm;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (abs(spin[i])==1) eradius[i] += dtv * ervel[i];
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
if (abs(spin[i])==1) {
ervel[i] += dtfm * erforce[i] / mefactor;
eradius[i] += dtv * ervel[i];
}
}
}
/* ----------------------------------------------------------------------

4
src/GPU/pair_sph_heatconduction_gpu.cpp
View File

@ -113,7 +113,7 @@ void PairSPHHeatConductionGPU::compute(int eflag, int vflag)
neighbor->ago, inum, nall, atom->x, atom->type,
sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag,
eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v);
cpu_time, success, atom->vest);
} else {
inum = list->inum;
ilist = list->ilist;
@ -122,7 +122,7 @@ void PairSPHHeatConductionGPU::compute(int eflag, int vflag)
sph_heatconduction_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start, cpu_time, success,
atom->tag, atom->v);
atom->tag, atom->vest);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");

28
src/GPU/pair_sph_lj_gpu.cpp
View File

@ -114,7 +114,7 @@ void PairSPHLJGPU::compute(int eflag, int vflag)
neighbor->ago, inum, nall, atom->x, atom->type,
sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag,
eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v);
cpu_time, success, atom->vest);
} else {
inum = list->inum;
ilist = list->ilist;
@ -123,7 +123,7 @@ void PairSPHLJGPU::compute(int eflag, int vflag)
sph_lj_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start, cpu_time, success,
atom->tag, atom->v);
atom->tag, atom->vest);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
@ -136,21 +136,21 @@ void PairSPHLJGPU::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
if (acc_float) {
auto drhoE_ptr = (float *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
for (int i = 0; i < nlocal; i++)
drho[i] += drhoE_ptr[i];
drhoE_ptr += nlocal;
for (int i = 0; i < nlocal; i++)
desph[i] += drhoE_ptr[i];
} else {
auto drhoE_ptr = (double *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
for (int i = 0; i < nlocal; i++)
drho[i] += drhoE_ptr[i];
drhoE_ptr += nlocal;
for (int i = 0; i < nlocal; i++)
desph[i] += drhoE_ptr[i];
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)

48
src/GPU/pair_sph_taitwater_gpu.cpp
View File

@ -18,6 +18,7 @@
#include "pair_sph_taitwater_gpu.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
@ -85,6 +86,25 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
// check consistency of pair coefficients
if (first) {
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = 1; i <= atom->ntypes; i++) {
if (cutsq[i][j] > 1.e-32) {
if (!setflag[i][i] || !setflag[j][j]) {
if (comm->me == 0) {
printf(
"SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n",
i, j, sqrt(cutsq[i][j]));
}
}
}
}
}
first = 0;
}
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
@ -110,7 +130,7 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag)
firstneigh = sph_taitwater_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v);
cpu_time, success, atom->vest);
} else {
inum = list->inum;
ilist = list->ilist;
@ -118,7 +138,7 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
sph_taitwater_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success,
atom->tag, atom->v);
atom->tag, atom->vest);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
@ -131,21 +151,21 @@ void PairSPHTaitwaterGPU::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
if (acc_float) {
auto drhoE_ptr = (float *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
for (int i = 0; i < nlocal; i++)
drho[i] += drhoE_ptr[i];
drhoE_ptr += nlocal;
for (int i = 0; i < nlocal; i++)
desph[i] += drhoE_ptr[i];
} else {
auto drhoE_ptr = (double *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
for (int i = 0; i < nlocal; i++)
drho[i] += drhoE_ptr[i];
drhoE_ptr += nlocal;
for (int i = 0; i < nlocal; i++)
desph[i] += drhoE_ptr[i];
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)

13
src/KOKKOS/pair_kokkos.h
View File

@ -950,6 +950,8 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P
static int vectorsize = 0;
static int atoms_per_team = 0;
static int teamsize_max_for = 0;
static int teamsize_max_reduce = 0;
#if defined(LMP_KOKKOS_GPU)
static int lastcall = -1;
@ -966,7 +968,6 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P
vectorsize = MIN(vectorsize,max_vectorsize);
int teamsize_max_for,teamsize_max_reduce;
if (fpair->atom->ntypes > MAX_TYPES_STACKPARAMS) {
PairComputeFunctor<PairStyle,NEIGHFLAG,false,ZEROFLAG,Specialisation > ff(fpair,list);
GetMaxTeamSize<typename PairStyle::device_type>(ff, inum, teamsize_max_for, teamsize_max_reduce);
@ -974,12 +975,12 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P
PairComputeFunctor<PairStyle,NEIGHFLAG,true,ZEROFLAG,Specialisation > ff(fpair,list);
GetMaxTeamSize<typename PairStyle::device_type>(ff, inum, teamsize_max_for, teamsize_max_reduce);
}
int teamsize_max = teamsize_max_for;
if (fpair->eflag || fpair->vflag)
teamsize_max = teamsize_max_reduce;
atoms_per_team = teamsize_max/vectorsize;
}
int teamsize_max = teamsize_max_for;
if (fpair->eflag || fpair->vflag)
teamsize_max = teamsize_max_reduce;
atoms_per_team = teamsize_max/vectorsize;
#else
vectorsize = 1;
atoms_per_team = 1;

18
src/MC/fix_sgcmc.cpp
View File

@ -253,11 +253,9 @@ void FixSemiGrandCanonicalMC::init()
error->all(FLERR, "Can not run fix sgcmc with naive total energy calculation "
"and more than one MPI process.");
// Create a compute that will provide the total energy of the system.
// Get reference to a compute that will provide the total energy of the system.
// This is needed by computeTotalEnergy().
char* id_pe = (char*)"thermo_pe";
int ipe = modify->find_compute(id_pe);
compute_pe = modify->compute[ipe];
compute_pe = modify->get_compute_by_id("thermo_pe");
}
interactionRadius = force->pair->cutforce;
if (comm->me == 0) utils::logmesg(lmp, " SGC - Interaction radius: {}\n", interactionRadius);
@ -373,8 +371,7 @@ void FixSemiGrandCanonicalMC::doMC()
// Use a random number to choose the new species if there are three or more atom types.
newSpecies = (int)(localRandom->uniform() * (atom->ntypes-1)) + 1;
if (newSpecies >= oldSpecies) newSpecies++;
}
else {
} else {
// If there are only two atom types, then the decision is clear.
newSpecies = (oldSpecies == 1) ? 2 : 1;
}
@ -394,8 +391,7 @@ void FixSemiGrandCanonicalMC::doMC()
if (serialMode && kappa != 0.0) {
for (int i = 2; i <= atom->ntypes; i++)
dm += (deltamu[i] + kappa / atom->natoms * (2.0 * speciesCounts[i] + deltaN[i])) * deltaN[i];
}
else {
} else {
for (int i = 2; i <= atom->ntypes; i++)
dm += deltamu[i] * deltaN[i];
}
@ -436,8 +432,7 @@ void FixSemiGrandCanonicalMC::doMC()
// Update global species counters.
for (int i = 1; i <= atom->ntypes; i++)
speciesCounts[i] += deltaNGlobal[i];
}
else if (serialMode) {
} else if (serialMode) {
// Update the local species counters.
for (int i = 1; i <= atom->ntypes; i++)
speciesCounts[i] += deltaN[i];
@ -450,8 +445,7 @@ void FixSemiGrandCanonicalMC::doMC()
else
flipAtomGeneric(selectedAtom, oldSpecies, newSpecies);
nAcceptedSwapsLocal++;
}
else {
} else {
nRejectedSwapsLocal++;
}

116
src/REPLICA/fix_pimd_langevin.cpp
View File

@ -47,10 +47,10 @@
using namespace LAMMPS_NS;
using namespace FixConst;
using MathConst::MY_PI;
using MathConst::MY_2PI;
using MathConst::THIRD;
using MathConst::MY_PI;
using MathConst::MY_SQRT2;
using MathConst::THIRD;
using MathSpecial::powint;
enum { PIMD, NMPIMD };
@ -475,11 +475,13 @@ void FixPIMDLangevin::init()
c_pe = modify->get_compute_by_id(id_pe);
if (!c_pe)
error->universe_all(FLERR, fmt::format("Could not find fix {} potential energy compute ID {}", style, id_pe));
error->universe_all(
FLERR, fmt::format("Could not find fix {} potential energy compute ID {}", style, id_pe));
c_press = modify->get_compute_by_id(id_press);
if (!c_press)
error->universe_all(FLERR, fmt::format("Could not find fix {} pressure compute ID {}", style, id_press));
error->universe_all(
FLERR, fmt::format("Could not find fix {} pressure compute ID {}", style, id_press));
t_prim = t_vir = t_cv = p_prim = p_vir = p_cv = p_md = 0.0;
}
@ -667,27 +669,26 @@ void FixPIMDLangevin::post_force(int /*flag*/)
imageint *image = atom->image;
tagint *tag = atom->tag;
if (method == NMPIMD) {
if (atom->nmax > maxunwrap) reallocate_x_unwrap();
if (atom->nmax > maxxc) reallocate_xc();
for (int i = 0; i < nlocal; i++) {
x_unwrap[i][0] = x[i][0];
x_unwrap[i][1] = x[i][1];
x_unwrap[i][2] = x[i][2];
}
if (mapflag) {
for (int i = 0; i < nlocal; i++) { domain->unmap(x_unwrap[i], image[i]); }
}
for (int i = 0; i < nlocal; i++) {
xc[i][0] = xcall[3 * (tag[i] - 1) + 0];
xc[i][1] = xcall[3 * (tag[i] - 1) + 1];
xc[i][2] = xcall[3 * (tag[i] - 1) + 2];
}
compute_vir();
compute_cvir();
compute_t_vir();
if (atom->nmax > maxunwrap) reallocate_x_unwrap();
if (atom->nmax > maxxc) reallocate_xc();
for (int i = 0; i < nlocal; i++) {
x_unwrap[i][0] = x[i][0];
x_unwrap[i][1] = x[i][1];
x_unwrap[i][2] = x[i][2];
}
if (mapflag) {
for (int i = 0; i < nlocal; i++) { domain->unmap(x_unwrap[i], image[i]); }
}
for (int i = 0; i < nlocal; i++) {
xc[i][0] = xcall[3 * (tag[i] - 1) + 0];
xc[i][1] = xcall[3 * (tag[i] - 1) + 1];
xc[i][2] = xcall[3 * (tag[i] - 1) + 2];
}
compute_vir();
compute_xf_vir();
compute_cvir();
compute_t_vir();
if (method == PIMD) {
if (mapflag) {
@ -696,6 +697,7 @@ void FixPIMDLangevin::post_force(int /*flag*/)
inter_replica_comm(x);
spring_force();
compute_spring_energy();
compute_t_prim();
if (mapflag) {
for (int i = 0; i < nlocal; i++) { domain->unmap_inv(x[i], image[i]); }
}
@ -741,7 +743,7 @@ void FixPIMDLangevin::collect_xc()
}
}
const double sqrtnp = sqrt((double)np);
const double sqrtnp = sqrt((double) np);
for (int i = 0; i < nlocal; i++) {
xcall[3 * (tag[i] - 1) + 0] = x[i][0] / sqrtnp;
xcall[3 * (tag[i] - 1) + 1] = x[i][1] / sqrtnp;
@ -1048,8 +1050,8 @@ void FixPIMDLangevin::langevin_init()
c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]);
}
for (int i = 0; i < np; i++) {
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i,
_omega_k[i], tau_k[i], c1_k[i], c2_k[i]);
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i],
c1_k[i], c2_k[i]);
}
} else if (method == PIMD) {
for (int i = 0; i < np; i++) {
@ -1111,7 +1113,7 @@ void FixPIMDLangevin::nmpimd_init()
}
// Set up eigenvectors for degenerated modes
const double sqrtnp = sqrt((double)np);
const double sqrtnp = sqrt((double) np);
for (int j = 0; j < np; j++) {
for (int i = 1; i < int(np / 2) + 1; i++) {
M_x2xp[i][j] = MY_SQRT2 * cos(MY_2PI * double(i) * double(j) / double(np)) / sqrtnp;
@ -1364,7 +1366,23 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
void FixPIMDLangevin::remove_com_motion()
{
if (universe->iworld == 0) {
if (method == NMPIMD) {
if (universe->iworld == 0) {
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (dynamic) masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup, masstotal, vcm);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] -= vcm[0];
v[i][1] -= vcm[1];
v[i][2] -= vcm[2];
}
}
}
} else if (method == PIMD) {
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -1378,24 +1396,34 @@ void FixPIMDLangevin::remove_com_motion()
v[i][2] -= vcm[2];
}
}
} else {
error->all(FLERR, "Unknown method for fix pimd/langevin. Only nmpimd and pimd are supported!");
}
}
/* ---------------------------------------------------------------------- */
void FixPIMDLangevin::compute_xf_vir()
{
int nlocal = atom->nlocal;
double xf = 0.0;
vir_ = 0.0;
for (int i = 0; i < nlocal; i++) {
for (int j = 0; j < 3; j++) { xf += x_unwrap[i][j] * atom->f[i][j]; }
}
MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
}
/* ---------------------------------------------------------------------- */
void FixPIMDLangevin::compute_cvir()
{
int nlocal = atom->nlocal;
double xf = 0.0;
double xcf = 0.0;
vir_ = centroid_vir = 0.0;
centroid_vir = 0.0;
for (int i = 0; i < nlocal; i++) {
for (int j = 0; j < 3; j++) {
xf += x_unwrap[i][j] * atom->f[i][j];
xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j];
}
for (int j = 0; j < 3; j++) { xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j]; }
}
MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
MPI_Allreduce(&xcf, &centroid_vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
if (pstyle == ANISO) {
for (int i = 0; i < 6; i++) c_vir_tensor[i] = 0.0;
@ -1553,11 +1581,19 @@ void FixPIMDLangevin::compute_p_prim()
void FixPIMDLangevin::compute_p_cv()
{
double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
if (universe->iworld == 0) {
p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np;
}
p_md = THIRD * inv_volume * (totke + vir);
MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
if (method == NMPIMD) {
if (universe->iworld == 0) {
p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np;
}
MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
} else if (method == PIMD) {
p_cv = THIRD * inv_volume * ((2.0 * totke / np - centroid_vir) * force->nktv2p + vir) / np;
} else {
error->universe_all(
FLERR,
"Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
}
}
/* ---------------------------------------------------------------------- */

1
src/REPLICA/fix_pimd_langevin.h
View File

@ -176,6 +176,7 @@ class FixPIMDLangevin : public Fix {
void compute_p_prim();
void compute_p_cv(); // centroid-virial pressure estimator
void compute_vir();
void compute_xf_vir();
void compute_cvir();
void compute_totenthalpy();

3
src/SPIN/compute_spin.cpp
View File

@ -215,9 +215,8 @@ void ComputeSpin::compute_vector()
tempnum += tx*tx+ty*ty+tz*tz;
tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2];
countsp++;
}
} else error->all(FLERR,"Compute compute/spin requires atom/spin style");
}
else error->all(FLERR,"Compute compute/spin requires atom/spin style");
}
MPI_Allreduce(mag,magtot,4,MPI_DOUBLE,MPI_SUM,world);

2
src/angle_hybrid.cpp
View File

@ -270,7 +270,7 @@ void AngleHybrid::coeff(int narg, char **arg)
else if (strcmp(arg[1], "bb") == 0)
error->all(FLERR, "BondBond coeff for hybrid angle has invalid format");
else
error->all(FLERR, "Angle coeff for hybrid has invalid style");
error->all(FLERR, "Expected hybrid sub-style instead of {} in angle_coeff command", arg[1]);
}
// move 1st arg to 2nd arg

2
src/bond_hybrid.cpp
View File

@ -305,7 +305,7 @@ void BondHybrid::coeff(int narg, char **arg)
if (strcmp(arg[1], "none") == 0)
none = 1;
else
error->all(FLERR, "Bond coeff for hybrid has invalid style");
error->all(FLERR, "Expected hybrid sub-style instead of {} in bond_coeff command", arg[1]);
}
// move 1st arg to 2nd arg

3
src/dihedral_hybrid.cpp
View File

@ -277,7 +277,8 @@ void DihedralHybrid::coeff(int narg, char **arg)
else if (strcmp(arg[1], "bb13") == 0)
error->all(FLERR, "BondBond13 coeff for hybrid dihedral has invalid format");
else
error->all(FLERR, "Dihedral coeff for hybrid has invalid style");
error->all(FLERR, "Expected hybrid sub-style instead of {} in dihedral_coeff command",
arg[1]);
}
// move 1st arg to 2nd arg

8
src/fix_ave_chunk.cpp
View File

@ -193,10 +193,12 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk file", error);
} else if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) {
if (iarg+2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ave/chunk ")+arg[iarg], error);
if (comm->me == 0) {
fp = fopen(arg[iarg+1],"w");
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if (fp == nullptr)
error->one(FLERR, "Cannot open fix ave/chunk file {}: {}",
arg[iarg+1], utils::getsyserror());

8
src/fix_ave_histo.cpp
View File

@ -839,10 +839,12 @@ void FixAveHisto::options(int iarg, int narg, char **arg)
auto mycmd = fmt::format("fix {}", style);
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " file", error);
if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) {
if (iarg+2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ave/histo ")+arg[iarg], error);
if (comm->me == 0) {
fp = fopen(arg[iarg+1],"w");
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if (fp == nullptr)
error->one(FLERR, "Cannot open fix ave/histo file {}: {}",
arg[iarg+1], utils::getsyserror());

35
src/fix_ave_time.cpp
View File

@ -1033,41 +1033,44 @@ void FixAveTime::options(int iarg, int narg, char **arg)
// optional args
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) {
if (iarg+2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ave/time ")+arg[iarg], error);
yaml_flag = utils::strmatch(arg[iarg+1],"\\.[yY][aA]?[mM][lL]$");
if (comm->me == 0) {
fp = fopen(arg[iarg+1],"w");
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix ave/time file {}: {}",
arg[iarg+1], utils::getsyserror());
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time ave", error);
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/time command");
else error->all(FLERR,"Unknown fix ave/time ave keyword {}", arg[iarg+1]);
if (ave == WINDOW) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix ave/time ave window", error);
nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/time command");
if (nwindow <= 0)
error->all(FLERR,"Illegal fix ave/time ave window argument {}; must be > 0", nwindow);
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time start", error);
startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time mode", error);
if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR;
else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR;
else error->all(FLERR,"Illegal fix ave/time command");
else error->all(FLERR,"Unknown fix ave/time mode {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"off") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time off", error);
memory->grow(offlist,noff+1,"ave/time:offlist");
offlist[noff++] = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
@ -1075,27 +1078,27 @@ void FixAveTime::options(int iarg, int narg, char **arg)
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time format", error);
delete[] format_user;
format_user = utils::strdup(arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title1", error);
delete[] title1;
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title2", error);
delete[] title2;
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/time title3", error);
delete[] title3;
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Unknown fix ave/time command option {}", arg[iarg]);
} else error->all(FLERR,"Unknown fix ave/time keyword {}", arg[iarg]);
}
}

103
src/fix_print.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,6 +13,7 @@
#include "fix_print.h"
#include "comm.h"
#include "error.h"
#include "input.h"
#include "memory.h"
@ -29,24 +29,22 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
fp(nullptr), text(nullptr), copy(nullptr), work(nullptr), var_print(nullptr)
Fix(lmp, narg, arg), fp(nullptr), text(nullptr), copy(nullptr), work(nullptr),
var_print(nullptr)
{
if (narg < 5) error->all(FLERR,"Illegal fix print command");
if (utils::strmatch(arg[3],"^v_")) {
var_print = utils::strdup(arg[3]+2);
if (narg < 5) utils::missing_cmd_args(FLERR, "fix print", error);
if (utils::strmatch(arg[3], "^v_")) {
var_print = utils::strdup(arg[3] + 2);
nevery = 1;
} else {
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix print command");
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
if (nevery <= 0) error->all(FLERR, "Illegal fix print nevery value {}; must be > 0", nevery);
}
MPI_Comm_rank(world,&me);
text = utils::strdup(arg[4]);
int n = strlen(text)+1;
copy = (char *) memory->smalloc(n*sizeof(char),"fix/print:copy");
work = (char *) memory->smalloc(n*sizeof(char),"fix/print:work");
int n = strlen(text) + 1;
copy = (char *) memory->smalloc(n * sizeof(char), "fix/print:copy");
work = (char *) memory->smalloc(n * sizeof(char), "fix/print:work");
maxcopy = maxwork = n;
// parse optional args
@ -57,48 +55,54 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0 || strcmp(arg[iarg],"append") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command");
if (me == 0) {
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if ((strcmp(arg[iarg], "file") == 0) || (strcmp(arg[iarg], "append") == 0)) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix print ") + arg[iarg], error);
if (comm->me == 0) {
if (strcmp(arg[iarg], "file") == 0)
fp = fopen(arg[iarg + 1], "w");
else
fp = fopen(arg[iarg + 1], "a");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix print file {}: {}",
arg[iarg+1], utils::getsyserror());
error->one(FLERR, "Cannot open fix print file {}: {}", arg[iarg + 1],
utils::getsyserror());
}
iarg += 2;
} else if (strcmp(arg[iarg],"screen") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command");
screenflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
} else if (strcmp(arg[iarg], "screen") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix print screen", error);
screenflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"title") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command");
delete [] title;
title = utils::strdup(arg[iarg+1]);
} else if (strcmp(arg[iarg], "title") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix print title", error);
delete[] title;
title = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix print command");
} else
error->all(FLERR, "Unknown fix print keyword: {}", arg[iarg]);
}
// print file comment line
if (fp && me == 0) {
if (title) fprintf(fp,"%s\n",title);
else fprintf(fp,"# Fix print output for fix %s\n",id);
if (fp && (comm->me == 0)) {
if (title)
fprintf(fp, "%s\n", title);
else
fprintf(fp, "# Fix print output for fix %s\n", id);
}
delete [] title;
delete[] title;
}
/* ---------------------------------------------------------------------- */
FixPrint::~FixPrint()
{
delete [] text;
delete [] var_print;
delete[] text;
delete[] var_print;
memory->sfree(copy);
memory->sfree(work);
if (fp && me == 0) fclose(fp);
if (fp && (comm->me == 0)) fclose(fp);
}
/* ---------------------------------------------------------------------- */
@ -117,16 +121,16 @@ void FixPrint::init()
if (var_print) {
ivar_print = input->variable->find(var_print);
if (ivar_print < 0)
error->all(FLERR,"Variable name for fix print timestep does not exist");
error->all(FLERR, "Variable {} for fix print timestep does not exist", var_print);
if (!input->variable->equalstyle(ivar_print))
error->all(FLERR,"Variable for fix print timestep is invalid style");
next_print = static_cast<bigint>
(input->variable->compute_equal(ivar_print));
error->all(FLERR, "Variable {} for fix print timestep is invalid style", var_print);
next_print = static_cast<bigint>(input->variable->compute_equal(ivar_print));
if (next_print <= update->ntimestep)
error->all(FLERR,"Fix print timestep variable returned a bad timestep");
error->all(FLERR, "Fix print timestep variable {} returned a bad timestep: {}", var_print,
next_print);
} else {
if (update->ntimestep % nevery)
next_print = (update->ntimestep/nevery)*nevery + nevery;
next_print = (update->ntimestep / nevery) * nevery + nevery;
else
next_print = update->ntimestep;
}
@ -158,24 +162,23 @@ void FixPrint::end_of_step()
modify->clearstep_compute();
strncpy(copy,text,maxcopy);
input->substitute(copy,work,maxcopy,maxwork,0);
strncpy(copy, text, maxcopy);
input->substitute(copy, work, maxcopy, maxwork, 0);
if (var_print) {
next_print = static_cast<bigint>
(input->variable->compute_equal(ivar_print));
next_print = static_cast<bigint>(input->variable->compute_equal(ivar_print));
if (next_print <= update->ntimestep)
error->all(FLERR,"Fix print timestep variable returned a bad timestep");
error->all(FLERR, "Fix print timestep variable returned a bad timestep: {}", next_print);
} else {
next_print = (update->ntimestep/nevery)*nevery + nevery;
next_print = (update->ntimestep / nevery) * nevery + nevery;
}
modify->addstep_compute(next_print);
if (me == 0) {
if (screenflag) utils::logmesg(lmp,std::string(copy) + "\n");
if (comm->me == 0) {
if (screenflag) utils::logmesg(lmp, std::string(copy) + "\n");
if (fp) {
fmt::print(fp,"{}\n",copy);
fmt::print(fp, "{}\n", copy);
fflush(fp);
}
}

2
src/fix_print.h
View File

@ -34,7 +34,7 @@ class FixPrint : public Fix {
void end_of_step() override;
private:
int me, screenflag;
int screenflag;
FILE *fp;
char *text, *copy, *work;
int maxcopy, maxwork;

3
src/improper_hybrid.cpp
View File

@ -269,7 +269,8 @@ void ImproperHybrid::coeff(int narg, char **arg)
else if (strcmp(arg[1], "aa") == 0)
error->all(FLERR, "AngleAngle coeff for hybrid improper has invalid format");
else
error->all(FLERR, "Improper coeff for hybrid has invalid style");
error->all(FLERR, "Expected hybrid sub-style instead of {} in improper_coeff command",
arg[1]);
}
// move 1st arg to 2nd arg

65
src/library.cpp
View File

@ -2137,7 +2137,8 @@ available.
.. code-block:: c
double *dptr = (double *) lammps_extract_fix(handle,name,0,1,0,0);
double *dptr = (double *) lammps_extract_fix(handle, name,
LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0);
double value = *dptr;
lammps_free((void *)dptr);
@ -2857,10 +2858,6 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
if ((count == 1) || imgunpack) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@ -2868,11 +2865,13 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(vector,nlocal,MPI_INT,data,recvcounts,displs,
MPI_INT,lmp->world);
MPI_Allgatherv(vector,nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world);
} else if (imgunpack) {
lmp->memory->create(copy,count*nlocal,"lib/gather:copy");
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
offset = 0;
for (i = 0; i < nlocal; i++) {
const int image = vector[i];
@ -2885,8 +2884,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(copy,count*nlocal,MPI_INT,
data,recvcounts,displs,MPI_INT,lmp->world);
MPI_Allgatherv(copy,count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world);
lmp->memory->destroy(copy);
} else {
@ -2895,8 +2893,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,
data,recvcounts,displs,MPI_INT,lmp->world);
MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world);
}
} else {
@ -2912,8 +2909,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(vector,nlocal,MPI_DOUBLE,data,recvcounts,displs,
MPI_DOUBLE,lmp->world);
MPI_Allgatherv(vector,nlocal,MPI_DOUBLE,data,recvcounts,displs,MPI_DOUBLE,lmp->world);
} else {
int n = count*nlocal;
@ -3171,10 +3167,6 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count,
return;
}
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = nullptr;
int **array = nullptr;
@ -3322,10 +3314,6 @@ void lammps_scatter_atoms_subset(void *handle, const char *name, int type,
return;
}
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = nullptr;
int **array = nullptr;
@ -4328,10 +4316,6 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
if ((count == 1) || imgunpack) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@ -4343,7 +4327,10 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
MPI_INT,lmp->world);
} else if (imgunpack) {
lmp->memory->create(copy,count*nlocal,"lib/gather:copy");
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
offset = 0;
for (i = 0; i < nlocal; i++) {
const int image = vector[i];
@ -4356,8 +4343,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(copy,count*nlocal,MPI_INT,
data,recvcounts,displs,MPI_INT,lmp->world);
MPI_Allgatherv(copy,count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world);
lmp->memory->destroy(copy);
} else {
@ -4366,8 +4352,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
displs[0] = 0;
for (i = 1; i < nprocs; i++)
displs[i] = displs[i-1] + recvcounts[i-1];
MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,
data,recvcounts,displs,MPI_INT,lmp->world);
MPI_Allgatherv(&array[0][0],count*nlocal,MPI_INT,data,recvcounts,displs,MPI_INT,lmp->world);
}
} else {
@ -4876,10 +4861,6 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
return;
}
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = nullptr;
int **array = nullptr;
@ -5130,10 +5111,6 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
return;
}
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = nullptr;
int **array = nullptr;
@ -5490,7 +5467,8 @@ int lammps_neighlist_num_elements(void *handle, int idx) {
* \param[out] numneigh number of neighbors of atom iatom or 0
* \param[out] neighbors pointer to array of neighbor atom local indices or NULL */
void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, int *numneigh, int **neighbors) {
void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom,
int *numneigh, int **neighbors) {
auto lmp = (LAMMPS *) handle;
Neighbor * neighbor = lmp->neighbor;
*iatom = -1;
@ -5777,9 +5755,7 @@ otherwise 0.
* \param setting string with the name of the specific setting
* \return 1 if available, 0 if not.
*/
int lammps_config_accelerator(const char *package,
const char *category,
const char *setting)
int lammps_config_accelerator(const char *package, const char *category, const char *setting)
{
return Info::has_accelerator_feature(package,category,setting) ? 1 : 0;
}
@ -5901,8 +5877,7 @@ int lammps_style_count(void *handle, const char *category) {
* \param buf_size size of the provided string buffer
* \return 1 if successful, otherwise 0
*/
int lammps_style_name(void *handle, const char *category, int idx,
char *buffer, int buf_size) {
int lammps_style_name(void *handle, const char *category, int idx, char *buffer, int buf_size) {
auto lmp = (LAMMPS *) handle;
Info info(lmp);
auto styles = info.get_available_styles(category);

6
src/pair_hybrid.cpp
View File

@ -521,8 +521,10 @@ void PairHybrid::coeff(int narg, char **arg)
int none = 0;
if (m == nstyles) {
if (strcmp(arg[2],"none") == 0) none = 1;
else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}", arg[2]);
if (strcmp(arg[2],"none") == 0)
none = 1;
else
error->all(FLERR,"Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]);
}
// move 1st/2nd args to 2nd/3rd args

6
src/pair_hybrid_overlay.cpp
View File

@ -59,8 +59,10 @@ void PairHybridOverlay::coeff(int narg, char **arg)
int none = 0;
if (m == nstyles) {
if (strcmp(arg[2],"none") == 0) none = 1;
else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}", arg[2]);
if (strcmp(arg[2],"none") == 0)
none = 1;
else
error->all(FLERR,"Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]);
}
// move 1st/2nd args to 2nd/3rd args

2
src/pair_hybrid_scaled.cpp
View File

@ -516,7 +516,7 @@ void PairHybridScaled::coeff(int narg, char **arg)
if (strcmp(arg[2], "none") == 0)
none = 1;
else
error->all(FLERR, "Pair coeff for hybrid has invalid style: {}", arg[2]);
error->all(FLERR, "Expected hybrid sub-style instead of {} in pair_coeff command", arg[2]);
}
// move 1st/2nd args to 2nd/3rd args

10
src/variable.cpp
View File

@ -1657,17 +1657,19 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (!compute->array_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (compute->size_array_rows == 0)
print_var_error(FLERR,"Variable formula compute array is zero length",ivar);
if (index1 > compute->size_array_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (index1 > compute->size_array_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
}
// wait until after compute invocation to check size_array_rows
// b/c may be zero until after initial invocation
if (compute->size_array_rows == 0)
print_var_error(FLERR,"Variable formula compute array is zero length",ivar);
auto newtree = new Tree();
newtree->type = VECTORARRAY;