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Merge pull request #4134 from akohlmey/collected-small-changes

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Collected small changes and bugfixes
This commit is contained in:
Axel Kohlmeyer
2024-04-17 00:35:57 -04:00
committed by GitHub
parent 329d546eea 101a937870
commit 3a555c81b6
17 changed files with 408 additions and 276 deletions
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25
doc/src/Howto_type_labels.rst
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@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box Ntypes for each interaction is "locked in" when the simulation box
is created. is created.
A recent addition to LAMMPS is the option to use strings - referred A recent addition to LAMMPS is the option to use strings - referred to
to as type labels - as an alternative. Using type labels instead of as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example, numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through type labels can make inputs more readable and generic (i.e. usable
the :doc:`include command <include>` for different systems with different through the :doc:`include command <include>` for different systems with
numerical values assigned to types. This generality also applies to different numerical values assigned to types. This generality also
other inputs like data files read by :doc:`read_data <read_data>` or applies to other inputs like data files read by :doc:`read_data
molecule template files read by the :doc:`molecule <molecule>` <read_data>` or molecule template files read by the :doc:`molecule
command. See below for a list of other commands that can use <molecule>` command. A discussion of the current type label support can
type labels in different ways. be found in :ref:`(Gissinger) <Typelabel24>`. See below for a list of
other commands that can use type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total that many previous restrictions still apply. For example, the total
@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without type labels, and results in templates that can be used without
modification in multiple simulations or different systems. modification in multiple simulations or different systems.
-----------
.. _Typelabel24:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

4
doc/src/Intro_features.rst
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@ -29,7 +29,7 @@ General features
* spatial decomposition of simulation domain for MPI parallelism * spatial decomposition of simulation domain for MPI parallelism
* particle decomposition inside spatial decomposition for OpenMP and GPU parallelism * particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
* GPLv2 licensed open-source distribution * GPLv2 licensed open-source distribution
* highly portable C++-11 * highly portable C++-11 (optional packages may require C++17)
* modular code with most functionality in optional packages * modular code with most functionality in optional packages
* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation * only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
* other libraries are optional and only required for specific packages * other libraries are optional and only required for specific packages
@ -81,7 +81,7 @@ commands)
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted * pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
* charged pairwise potentials: Coulombic, point-dipole * charged pairwise potentials: Coulombic, point-dipole
* many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta * many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN * machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP
* interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP * interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS * long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>` * polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`

17
doc/src/Python_scatter.rst
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@ -54,8 +54,21 @@ like this:
x[3] = x coord of atom with ID 2 x[3] = x coord of atom with ID 2
... ...
x[n3-1] = z coord of atom with ID natoms x[n3-1] = z coord of atom with ID natoms
lmp.scatter_atoms("x",1,3,x) lmp.scatter_atoms("x", 1, 3, x)
The coordinates can also be provided as arguments to the initializer of x:
.. code-block:: python
from ctypes import c_double
natoms = 2
n3 = 3*natoms
# init in constructor
x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0)
lmp.scatter_atoms("x", 1, 3, x)
# or using a list
coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0]
x = (c_double*len(coords))(*coords)
Alternatively, you can just change values in the vector returned by Alternatively, you can just change values in the vector returned by
the gather methods, since they are also ctypes vectors. the gather methods, since they are also ctypes vectors.

9
doc/src/labelmap.rst
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@ -43,7 +43,8 @@ The label map can also be defined by the :doc:`read_data <read_data>`
command when it reads these sections in a data file: Atom Type Labels, command when it reads these sections in a data file: Atom Type Labels,
Bond Type Labels, etc. See the :doc:`Howto type labels Bond Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for a general discussion of how type <Howto_type_labels>` doc page for a general discussion of how type
labels can be used. labels can be used. See :ref:`(Gissinger) <Typelabel>` for a discussion
of the type label implementation in LAMMPS and its uses.
Valid type labels can contain any alphanumeric character, but must not Valid type labels can contain any alphanumeric character, but must not
start with a number, a '#', or a '*' character. They can contain other start with a number, a '#', or a '*' character. They can contain other
@ -98,3 +99,9 @@ Default
""""""" """""""
none none
-----------
.. _Typelabel:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

15
doc/src/pair_eam.rst
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@ -140,6 +140,21 @@ The OpenKIM Project at
provides EAM potentials that can be used directly in LAMMPS with the provides EAM potentials that can be used directly in LAMMPS with the
:doc:`kim command <kim_commands>` interface. :doc:`kim command <kim_commands>` interface.
.. warning::
The EAM potential files tabulate the embedding energy as a function
of the local electron density :math:`\rho`. When atoms get too
close, this electron density may exceed the range for which the
embedding energy was tabulated for. To avoid crashes, LAMMPS will
assume a linearly increasing embedding energy for electron densities
beyond the maximum tabulated value. LAMMPS will print a warning when
this happens. It may be acceptable at the beginning of an
equilibration (e.g. when using randomized coordinates) but would be a
big concern for accuracy if it happens during production runs. The
EAM potential file triggering the warning during production is thus
not a good choice, and the EAM model in general not likely a good
model for the kind of system under investigation.
---------- ----------
For style *eam*, potential values are read from a file that is in the For style *eam*, potential values are read from a file that is in the

1
doc/utils/sphinx-config/false_positives.txt
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@ -492,6 +492,7 @@ ChiralIDs
chirality chirality
Cho Cho
Chodera Chodera
Choi
ChooseOffset ChooseOffset
chris chris
Christoph Christoph

4
examples/ttm/Si.ttm_mod
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@ -17,9 +17,9 @@ rho_e, electrons/volume units
D_e, length^2/time units D_e, length^2/time units
20000 20000
gamma_p, mass/time units gamma_p, mass/time units
39.235
gamma_s, mass/time units
24.443 24.443
gamma_s, mass/time units
39.235
v_0, length/time units v_0, length/time units
79.76 79.76
I_0, energy/(time*length^2) units I_0, energy/(time*length^2) units

43
examples/ttm/log.18May23.ttm.mod.g++.1 → examples/ttm/log.15Apr24.ttm.mod.g++.1
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@ -1,4 +1,5 @@
LAMMPS (28 Mar 2023 - Development) LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d)
using 1 OpenMP thread(s) per MPI task
units metal units metal
atom_style atomic atom_style atomic
boundary p p p boundary p p p
@ -13,7 +14,7 @@ mass 1 28.0855
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
Created 8000 atoms Created 8000 atoms
using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309) using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
create_atoms CPU = 0.002 seconds create_atoms CPU = 0.001 seconds
pair_style sw pair_style sw
pair_coeff * * Si.sw Si pair_coeff * * Si.sw Si
@ -79,30 +80,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2] Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -34692.79996100604 -52.79390940511979 0 0 0 -34692.79996100604 -52.79390940511979 0
100 2.004897156140836 -34690.27961013186 -55.3499730543189 0.01301140393178352 100 1.255921182965094 -34691.22889627319 -54.38067722556279 0.004868249873095404
200 2.837118035232607 -34687.74741132015 -57.93445748841876 0.02696025968760173 200 1.858362347834853 -34689.5405389424 -56.09419523244324 0.01649190747838086
300 4.263087164947482 -34684.98084093686 -60.75945453846793 0.02175636603841567 300 2.581575104085017 -34687.9650112138 -57.69350558275053 0.01683584513983131
400 5.568003854939066 -34682.25271040963 -63.56896518300499 0.03000618483472749 400 3.47533128765632 -34686.2796683925 -59.40465113478642 0.005727647825729662
500 6.225602451570786 -34679.49948952029 -66.40897551884574 0.02768827702656703 500 4.080137293185865 -34684.25857873315 -61.46449138661911 0.005828121949923951
600 7.608847536264781 -34676.69728436362 -69.32060611557282 0.05579466731854091 600 4.816104423494803 -34682.51412688349 -63.25804498666959 0.02397283419020746
700 9.049471241531297 -34674.00093206036 -72.10055094219462 0.004335980559879032 700 5.937291156573137 -34680.64941595491 -65.17152689673857 0.02604017750117964
800 9.826796099683211 -34671.27720242751 -74.95010610862134 0.02371649678091515 800 6.487028971399661 -34678.87151939966 -66.99420300650799 0.009720189851817886
900 11.8609224958918 -34668.35091308811 -77.98544170794545 0.004658649791374908 900 7.461479797687167 -34677.29259652842 -68.63442522233655 0.02576822683306545
1000 13.88037467640968 -34665.35025858006 -81.16445160194111 0.07684078334464743 1000 8.696444335455215 -34675.39247806347 -70.59264558122587 0.0147252863003017
Loop time of 2.48942 on 1 procs for 1000 steps with 8000 atoms Loop time of 5.11497 on 1 procs for 1000 steps with 8000 atoms
Performance: 3.471 ns/day, 6.915 hours/ns, 401.700 timesteps/s, 3.214 Matom-step/s Performance: 1.689 ns/day, 14.208 hours/ns, 195.505 timesteps/s, 1.564 Matom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.126 | 2.126 | 2.126 | 0.0 | 85.40 Pair | 4.3498 | 4.3498 | 4.3498 | 0.0 | 85.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016147 | 0.016147 | 0.016147 | 0.0 | 0.65 Comm | 0.037981 | 0.037981 | 0.037981 | 0.0 | 0.74
Output | 0.0013116 | 0.0013116 | 0.0013116 | 0.0 | 0.05 Output | 0.0025641 | 0.0025641 | 0.0025641 | 0.0 | 0.05
Modify | 0.33864 | 0.33864 | 0.33864 | 0.0 | 13.60 Modify | 0.71279 | 0.71279 | 0.71279 | 0.0 | 13.94
Other | | 0.007318 | | | 0.29 Other | | 0.01179 | | | 0.23
Nlocal: 8000 ave 8000 max 8000 min Nlocal: 8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -117,4 +118,4 @@ Total # of neighbors = 272000
Ave neighs/atom = 34 Ave neighs/atom = 34
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:02 Total wall time: 0:00:05

42
examples/ttm/log.18May23.ttm.mod.g++.4 → examples/ttm/log.15Apr24.ttm.mod.g++.4
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@ -1,5 +1,5 @@
LAMMPS (28 Mar 2023 - Development) LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:531) using 1 OpenMP thread(s) per MPI task
units metal units metal
atom_style atomic atom_style atomic
boundary p p p boundary p p p
@ -14,7 +14,7 @@ mass 1 28.0855
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
Created 8000 atoms Created 8000 atoms
using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309) using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.002 seconds
pair_style sw pair_style sw
pair_coeff * * Si.sw Si pair_coeff * * Si.sw Si
@ -80,30 +80,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2] Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -34692.79996100361 -52.79390940511979 0 0 0 -34692.79996100361 -52.79390940511979 0
100 1.852689977101411 -34690.49204900486 -55.14271612882064 0.02726188676577098 100 1.20337355884597 -34691.30677367127 -54.30747356568817 0.01557346850238741
200 2.735750477179192 -34688.11139028054 -57.57110998717798 0.03387986355513584 200 1.709631732825883 -34689.83859944795 -55.7982356998371 0.02508386983502213
300 3.931848271449558 -34685.54667417785 -60.18684521127231 0.02261256315262403 300 2.488524478071323 -34688.26307995134 -57.3977272154369 0.02664346353990833
400 5.462009198576365 -34682.74455105668 -63.05420336037233 0.002402241637719578 400 3.38535890366476 -34686.51395648598 -59.17547816947624 0.02164200191836632
500 6.267811692893873 -34679.96493887379 -65.93304222280051 0.02448378880218699 500 3.838163353802383 -34684.79466673204 -60.92228950760077 0.005860499116196545
600 7.21148216150661 -34677.41455784726 -68.58391420045926 0.04114045759945374 600 4.675913079756001 -34683.03448988724 -62.72423959707044 0.0106700119158327
700 8.84660534187052 -34674.40610468235 -71.68798344296859 0.02372984027434538 700 5.637185532827328 -34681.25888274477 -64.5491928842093 0.01568536325219336
800 10.1748456457686 -34671.08749605772 -75.11943618276216 0.007538225788030307 800 6.316986413957468 -34679.29231578312 -66.57005328290739 0.02035373879569394
900 11.27479036162859 -34668.4118066423 -77.92921692176756 0.02537529314475071 900 7.211479047111087 -34677.61236020172 -68.30976417874265 0.03239086895076279
1000 13.26881394868076 -34665.56617589539 -80.91544540266317 0.03112665440209921 1000 8.431725106300505 -34675.81097854214 -70.161139196977 0.01219385884660358
Loop time of 0.995347 on 4 procs for 1000 steps with 8000 atoms Loop time of 1.73439 on 4 procs for 1000 steps with 8000 atoms
Performance: 8.680 ns/day, 2.765 hours/ns, 1004.675 timesteps/s, 8.037 Matom-step/s Performance: 4.982 ns/day, 4.818 hours/ns, 576.572 timesteps/s, 4.613 Matom-step/s
97.9% CPU use with 4 MPI tasks x no OpenMP threads 99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.65351 | 0.6616 | 0.66783 | 0.8 | 66.47 Pair | 1.127 | 1.1392 | 1.1511 | 1.0 | 65.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.041606 | 0.048314 | 0.056589 | 2.9 | 4.85 Comm | 0.068488 | 0.082304 | 0.094797 | 4.1 | 4.75
Output | 0.0014609 | 0.0014742 | 0.0014968 | 0.0 | 0.15 Output | 0.0024745 | 0.0025221 | 0.0025705 | 0.1 | 0.15
Modify | 0.27934 | 0.28016 | 0.28089 | 0.1 | 28.15 Modify | 0.50194 | 0.50329 | 0.50522 | 0.2 | 29.02
Other | | 0.003798 | | | 0.38 Other | | 0.007117 | | | 0.41
Nlocal: 2000 ave 2000 max 2000 min Nlocal: 2000 ave 2000 max 2000 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0

16
python/lammps/pylammps.py
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@ -192,11 +192,23 @@ class Atom(object):
@property @property
def mass(self): def mass(self):
""" """
Return the atom mass Return the atom mass as a per-atom property.
This returns either the per-type mass or the per-atom
mass (AKA 'rmass') depending on what is available with
preference for the per-atom mass.
.. versionchanged:: TBD
Support both per-type and per-atom masses. With
per-type return "mass[type[i]]" else return "rmass[i]".
Per-atom mass is preferred if available.
:type: float :type: float
""" """
return self.get("mass", self.type) if self._pylmp.lmp.extract_setting('rmass_flag'):
return self.get("rmass", self.index)
else:
return self.get("mass", self.type)
@property @property
def radius(self): def radius(self):

4
src/EXTRA-PAIR/pair_pedone.cpp
View File

@ -32,8 +32,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairPedone::PairPedone(LAMMPS *lmp) : PairPedone::PairPedone(LAMMPS *lmp) :
Pair(lmp), d0(nullptr), alpha(nullptr), r0(nullptr), c0(nullptr), pedone1(nullptr), Pair(lmp), cut(nullptr), d0(nullptr), alpha(nullptr), r0(nullptr), c0(nullptr),
pedone2(nullptr) pedone1(nullptr), pedone2(nullptr), offset(nullptr)
{ {
writedata = 1; writedata = 1;
} }

18
src/INTEL/pair_eam_intel.cpp
View File

@ -234,7 +234,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
const int istride = fc.rhor_istride(); const int istride = fc.rhor_istride();
const int jstride = fc.rhor_jstride(); const int jstride = fc.rhor_jstride();
const int fstride = fc.frho_stride(); const int fstride = fc.frho_stride();
int beyond_rhomax = 0;
{ {
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD) #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
*timer_compute = MIC_Wtime(); *timer_compute = MIC_Wtime();
@ -453,7 +453,10 @@ void PairEAMIntel::eval(const int offload, const int vflag,
if (EFLAG) { if (EFLAG) {
flt_t phi = ((frho_spline_e[ioff].a*p + frho_spline_e[ioff].b)*p + flt_t phi = ((frho_spline_e[ioff].a*p + frho_spline_e[ioff].b)*p +
frho_spline_e[ioff].c)*p + frho_spline_e[ioff].d; frho_spline_e[ioff].c)*p + frho_spline_e[ioff].d;
if (rho[i] > frhomax) phi += fp_f[i] * (rho[i]-frhomax); if (rho[i] > frhomax) {
phi += fp_f[i] * (rho[i]-frhomax);
beyond_rhomax = 1;
}
if (!ONETYPE) { if (!ONETYPE) {
const int ptr_off=itype*ntypes + itype; const int ptr_off=itype*ntypes + itype;
oscale = scale_f[ptr_off]; oscale = scale_f[ptr_off];
@ -653,6 +656,16 @@ void PairEAMIntel::eval(const int offload, const int vflag,
else else
fix->stop_watch(TIME_HOST_PAIR); fix->stop_watch(TIME_HOST_PAIR);
if (EFLAG && (!exceeded_rhomax)) {
MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_MAX, world);
if (exceeded_rhomax) {
if (comm->me == 0)
error->warning(FLERR,
"A per-atom density exceeded rhomax of EAM potential table - "
"a linear extrapolation to the energy was made");
}
}
if (EFLAG || vflag) if (EFLAG || vflag)
fix->add_result_array(f_start, ev_global, offload, eatom, 0, vflag); fix->add_result_array(f_start, ev_global, offload, eatom, 0, vflag);
else else
@ -849,4 +862,3 @@ void PairEAMIntel::unpack_forward_comm(int n, int first, double *buf,
last = first + n; last = first + n;
for (i = first; i < last; i++) fp_f[i] = buf[m++]; for (i = first; i < last; i++) fp_f[i] = buf[m++];
} }

19
src/MANYBODY/pair_eam.cpp
View File

@ -148,6 +148,8 @@ void PairEAM::compute(int eflag, int vflag)
evdwl = 0.0; evdwl = 0.0;
ev_init(eflag,vflag); ev_init(eflag,vflag);
int beyond_rhomax = 0;
// grow energy and fp arrays if necessary // grow energy and fp arrays if necessary
// need to be atom->nmax in length // need to be atom->nmax in length
@ -237,7 +239,10 @@ void PairEAM::compute(int eflag, int vflag)
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) { if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) {
phi += fp[i] * (rho[i]-rhomax);
beyond_rhomax = 1;
}
phi *= scale[type[i]][type[i]]; phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
@ -322,6 +327,16 @@ void PairEAM::compute(int eflag, int vflag)
} }
} }
if (eflag && (!exceeded_rhomax)) {
MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_MAX, world);
if (exceeded_rhomax) {
if (comm->me == 0)
error->warning(FLERR,
"A per-atom density exceeded rhomax of EAM potential table - "
"a linear extrapolation to the energy was made");
}
}
if (vflag_fdotr) virial_fdotr_compute(); if (vflag_fdotr) virial_fdotr_compute();
} }
@ -424,6 +439,8 @@ void PairEAM::init_style()
neighbor->add_request(this); neighbor->add_request(this);
embedstep = -1; embedstep = -1;
exceeded_rhomax = 0;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

3
src/MANYBODY/pair_eam.h
View File

@ -68,6 +68,9 @@ class PairEAM : public Pair {
double **scale; double **scale;
bigint embedstep; // timestep, the embedding term was computed bigint embedstep; // timestep, the embedding term was computed
int exceeded_rhomax; // global flag for whether rho[i] has exceeded rhomax
// on a step energy is computed - 0 = no, 1 = yes
// per-atom arrays // per-atom arrays
double *rho, *fp; double *rho, *fp;

17
src/OPENMP/pair_eam_omp.cpp
View File

@ -17,6 +17,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "error.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
@ -102,6 +103,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
double *coeff; double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh; int *ilist,*jlist,*numneigh,**firstneigh;
int beyond_rhomax = 0;
evdwl = 0.0; evdwl = 0.0;
const auto * _noalias const x = (dbl3_t *) atom->x[0]; const auto * _noalias const x = (dbl3_t *) atom->x[0];
@ -203,7 +205,10 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (EFLAG) { if (EFLAG) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) {
phi += fp[i] * (rho[i]-rhomax);
beyond_rhomax = 1;
}
e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr); e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr);
} }
} }
@ -298,6 +303,16 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
f[i].y += fytmp; f[i].y += fytmp;
f[i].z += fztmp; f[i].z += fztmp;
} }
if (EFLAG && (!exceeded_rhomax)) {
MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_MAX, world);
if (exceeded_rhomax) {
if (comm->me == 0)
error->warning(FLERR,
"A per-atom density exceeded rhomax of EAM potential table - "
"a linear extrapolation to the energy was made");
}
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

17
src/OPT/pair_eam_opt.cpp
View File

@ -23,6 +23,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "error.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
@ -118,6 +119,7 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void PairEAMOpt::eval()
int ntypes = atom->ntypes; int ntypes = atom->ntypes;
int ntypes2 = ntypes * ntypes; int ntypes2 = ntypes * ntypes;
int beyond_rhomax = 0;
auto *_noalias fast_alpha = auto *_noalias fast_alpha =
(fast_alpha_t *) malloc((size_t) ntypes2 * (nr + 1) * sizeof(fast_alpha_t)); (fast_alpha_t *) malloc((size_t) ntypes2 * (nr + 1) * sizeof(fast_alpha_t));
@ -251,7 +253,10 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void PairEAMOpt::eval()
fp[i] = (coeff[0] * p + coeff[1]) * p + coeff[2]; fp[i] = (coeff[0] * p + coeff[1]) * p + coeff[2];
if (EFLAG) { if (EFLAG) {
double phi = ((coeff[3] * p + coeff[4]) * p + coeff[5]) * p + coeff[6]; double phi = ((coeff[3] * p + coeff[4]) * p + coeff[5]) * p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i] - rhomax); if (rho[i] > rhomax) {
phi += fp[i] * (rho[i] - rhomax);
beyond_rhomax = 1;
}
phi *= scale[type[i]][type[i]]; phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
@ -361,5 +366,15 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void PairEAMOpt::eval()
free(fast_gamma); free(fast_gamma);
fast_gamma = nullptr; fast_gamma = nullptr;
if (EFLAG && (!exceeded_rhomax)) {
MPI_Allreduce(&beyond_rhomax, &exceeded_rhomax, 1, MPI_INT, MPI_MAX, world);
if (exceeded_rhomax) {
if (comm->me == 0)
error->warning(FLERR,
"A per-atom density exceeded rhomax of EAM potential table - "
"a linear extrapolation to the energy was made");
}
}
if (vflag_fdotr) virial_fdotr_compute(); if (vflag_fdotr) virial_fdotr_compute();
} }

430
src/library.cpp
View File

@ -527,7 +527,7 @@ void lammps_file(void *handle, const char *filename)
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
if (lmp->update->whichflag != 0) if (lmp->update->whichflag != 0)
lmp->error->all(FLERR, "Library error: issuing LAMMPS commands during a run is not allowed"); lmp->error->all(FLERR, "Issuing LAMMPS commands during a run is not allowed");
else else
lmp->input->file(filename); lmp->input->file(filename);
} }
@ -564,8 +564,7 @@ char *lammps_command(void *handle, const char *cmd)
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
if (lmp->update->whichflag != 0) if (lmp->update->whichflag != 0)
lmp->error->all(FLERR,"Library error: issuing LAMMPS commands " lmp->error->all(FLERR, "Issuing LAMMPS command during a run is not allowed.");
"during a run is not allowed.");
else else
result = lmp->input->one(cmd); result = lmp->input->one(cmd);
} }
@ -641,7 +640,7 @@ void lammps_commands_string(void *handle, const char *str)
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
if (lmp->update->whichflag != 0) { if (lmp->update->whichflag != 0) {
lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run"); lmp->error->all(FLERR, "Issuing LAMMPS commands during a run is not allowed");
} }
std::size_t cursor = 0; std::size_t cursor = 0;
@ -949,9 +948,9 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
// do nothing if box does not yet exist // do nothing if box does not yet exist
if ((lmp->domain->box_exist == 0) if (lmp->domain->box_exist == 0) {
&& (lmp->comm->me == 0)) { if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Calling lammps_extract_box without a box"); lmp->error->warning(FLERR, "Call to lammps_extract_box() without a box ignored");
return; return;
} }
@ -1011,12 +1010,12 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
if (lmp->atom->natoms > 0) if (lmp->atom->natoms > 0)
lmp->error->all(FLERR,"Calling lammps_reset_box not supported when atoms exist"); lmp->error->all(FLERR, "Calling lammps_reset_box() not supported when atoms exist");
// warn and do nothing if no box exists // warn and do nothing if no box exists
if (lmp->domain->box_exist == 0) { if (lmp->domain->box_exist == 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Ignoring call to lammps_reset_box without a box"); lmp->error->warning(FLERR,"Call to lammps_reset_box() without a box ignored");
return; return;
} }
@ -2629,7 +2628,14 @@ x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`);
*natoms*), as queried by :cpp:func:`lammps_get_natoms`, *natoms*), as queried by :cpp:func:`lammps_get_natoms`,
:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and consecutive.
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -2650,8 +2656,7 @@ This function is not compatible with ``-DLAMMPS_BIGBIG``.
Allreduce to sum vector into data across all procs Allreduce to sum vector into data across all procs
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void lammps_gather_atoms(void *handle, const char *name, int type, int count, void lammps_gather_atoms(void *handle, const char *name, int type, int count, void *data)
void *data)
{ {
auto lmp = (LAMMPS *) handle; auto lmp = (LAMMPS *) handle;
@ -2671,8 +2676,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count,
flag = 1; flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms(): Atom-IDs must exist and be consecutive");
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
return; return;
} }
@ -2680,8 +2684,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count,
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR, "lammps_gather_atoms(): unknown property {}", name);
lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
return; return;
} }
@ -2756,8 +2759,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count,
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world); MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy); lmp->memory->destroy(copy);
} else { } else {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms(): unsupported data type");
lmp->error->warning(FLERR,"lammps_gather_atoms: unsupported data type");
return; return;
} }
#endif #endif
@ -2785,10 +2787,17 @@ groups total, but not in order by atom ID (e.g., if *name* is *x* and *count*
is 3, then *data* might be something like x[10][0], x[10][1], x[10][2], is 3, then *data* might be something like x[10][0], x[10][1], x[10][2],
x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`); *data* must be x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`); *data* must be
pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as
queried by :cpp:func:`lammps_get_natoms`, queried by :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`,
:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. or :cpp:func:`lammps_extract_setting`.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined.
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -2828,8 +2837,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms_concat(): Atom-IDs must exist");
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
return; return;
} }
@ -2837,8 +2845,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms_concat(): unknown property {}", name);
lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
return; return;
} }
@ -2947,7 +2954,14 @@ x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], :math:`\dots`);
*data* must be pre-allocated by the caller to length *data* must be pre-allocated by the caller to length
(*count* :math:`\times` *ndata*). (*count* :math:`\times` *ndata*).
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and an :doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -2993,16 +3007,13 @@ void lammps_gather_atoms_subset(void *handle, const char *name, int type,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms_subset(): Atom-IDs must exist and be mapped");
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms_subset: atoms must have mappable ids");
return; return;
} }
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_atoms_subset(): unknown property {}", name);
lmp->error->warning(FLERR,"lammps_gather_atoms_subset: "
"unknown property name");
return; return;
} }
@ -3110,7 +3121,15 @@ atom ID (e.g., if *name* is *x* and *count* = 3, then
*data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0],
:math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*).
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined, must be consecutive, and an
:doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -3152,8 +3171,8 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_atoms(): "
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms: ids must exist, be consecutive, and be mapped"); "Atom-IDs must exist, be consecutive, and be mapped");
return; return;
} }
@ -3161,9 +3180,7 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count,
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR, "lammps_scatter_atoms(): unknown property {}", name);
lmp->error->warning(FLERR,
"lammps_scatter_atoms: unknown property name");
return; return;
} }
@ -3244,7 +3261,14 @@ to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2],
x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would
be {1, 100, 57}. be {1, 100, 57}.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and an :doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -3301,16 +3325,13 @@ void lammps_scatter_atoms_subset(void *handle, const char *name, int type,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_atoms_subset(): Atom-IDs must exist and be mapped");
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset: atoms must have mapped ids");
return; return;
} }
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR, "lammps_scatter_atoms_subset(): unknown property {}", name);
lmp->error->warning(FLERR,
"lammps_scatter_atoms_subset: unknown property name");
return; return;
} }
@ -3849,7 +3870,14 @@ The *data* array will be ordered in groups of *count* values, sorted by atom ID
This function will return an error if fix or compute data are requested and the fix or compute ID This function will return an error if fix or compute data are requested and the fix or compute ID
given does not have per-atom data. given does not have per-atom data.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and must be consecutive.
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -3899,7 +3927,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
lmp->error->all(FLERR,"Library function lammps_gather not compatible with -DLAMMPS_BIGBIG"); lmp->error->all(FLERR, "Library function lammps_gather() is not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,j,offset,ltype; int i,j,offset,ltype;
@ -3910,8 +3938,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
flag = 1; flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): Atom-IDs must exist, and be consecutive");
lmp->error->warning(FLERR,"Library error in lammps_gather");
return; return;
} }
@ -3921,28 +3948,25 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
// fix // fix
if (vptr==nullptr && utils::strmatch(name,"^f_")) { if (vptr==nullptr && utils::strmatch(name,"^f_")) {
const char *fixid = name+2;
auto fix = lmp->modify->get_fix_by_id(&name[2]); auto fix = lmp->modify->get_fix_by_id(fixid);
if (!fix) { if (!fix) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): unknown fix id {}", fixid);
lmp->error->warning(FLERR,"lammps_gather: unknown fix id");
return; return;
} }
if (fix->peratom_flag == 0) { if (fix->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): fix {} does not return peratom data", fixid);
lmp->error->warning(FLERR,"lammps_gather: fix does not return peratom data");
return; return;
} }
if ((count > 1) && (fix->size_peratom_cols != count)) { if ((count > 1) && (fix->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather: count != values peratom for fix {}", fixid);
lmp->error->warning(FLERR,"lammps_gather: count != values peratom for fix");
return; return;
} }
if (lmp->update->ntimestep % fix->peratom_freq) { if (lmp->update->ntimestep % fix->peratom_freq) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather: fix {} not computed at compatible time", fixid);
lmp->error->all(FLERR,"lammps_gather: fix not computed at compatible time");
return; return;
} }
@ -3953,22 +3977,19 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
// compute // compute
if (vptr==nullptr && utils::strmatch(name,"^c_")) { if (vptr==nullptr && utils::strmatch(name,"^c_")) {
const char *compid = name+2;
auto compute = lmp->modify->get_compute_by_id(&name[2]); auto compute = lmp->modify->get_compute_by_id(compid);
if (!compute) { if (!compute) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): unknown compute id {}", compid);
lmp->error->warning(FLERR,"lammps_gather: unknown compute id");
return; return;
} }
if (compute->peratom_flag == 0) { if (compute->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): compute {} does not return peratom data", compid);
lmp->error->warning(FLERR,"lammps_gather: compute does not return peratom data");
return; return;
} }
if ((count > 1) && (compute->size_peratom_cols != count)) { if ((count > 1) && (compute->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): count != values peratom for compute {}", compid);
lmp->error->warning(FLERR,"lammps_gather: count != values peratom for compute");
return; return;
} }
@ -3984,28 +4005,26 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
int idx,icol; int idx,icol;
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); const char *propid;
else idx = lmp->atom->find_custom(&name[3],ltype,icol); if (utils::strmatch(name,"^[id]_")) propid = name+2;
else propid = name+3;
idx = lmp->atom->find_custom(propid,ltype,icol);
if (idx < 0) { if (idx < 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): unknown property/atom id {}", propid);
lmp->error->warning(FLERR,"lammps_gather: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom type for {}", propid);
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom type");
return; return;
} }
if ((count == 1) && (icol != 0)) { if ((count == 1) && (icol != 0)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid);
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return; return;
} }
if ((count > 1) && (icol != count)) { if ((count > 1) && (icol != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid);
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return; return;
} }
@ -4021,8 +4040,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
// no match // no match
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather(): undefined property {}", name);
lmp->error->warning(FLERR,"lammps_gather: undefined property name");
return; return;
} }
@ -4122,7 +4140,14 @@ pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as quer
:cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or
:cpp:func:`lammps_extract_setting`. :cpp:func:`lammps_extract_setting`.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined.
The total number of atoms must be less than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -4173,8 +4198,8 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
lmp->error->all(FLERR,"Library function lammps_gather_concat" lmp->error->all(FLERR,"Library function lammps_gather_concat()"
" not compatible with -DLAMMPS_BIGBIG"); " is not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,offset,ltype; int i,offset,ltype;
@ -4184,8 +4209,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): atom-IDs must exist");
lmp->error->warning(FLERR,"Library error in lammps_gather_concat");
return; return;
} }
@ -4195,27 +4219,24 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
// fix // fix
if (vptr==nullptr && utils::strmatch(name,"^f_")) { if (vptr==nullptr && utils::strmatch(name,"^f_")) {
const char *fixid = name+2;
auto fix = lmp->modify->get_fix_by_id(&name[2]); auto fix = lmp->modify->get_fix_by_id(fixid);
if (!fix) { if (!fix) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): unknown fix id {}", fixid);
lmp->error->warning(FLERR,"lammps_gather_concat: unknown fix id");
return; return;
} }
if (fix->peratom_flag == 0) { if (fix->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): fix {} does not return peratom data", fixid);
lmp->error->warning(FLERR,"lammps_gather_concat: fix does not return peratom data");
return; return;
} }
if ((count > 1) && (fix->size_peratom_cols != count)) { if ((count > 1) && (fix->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for fix {}", fixid);
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for fix");
return; return;
} }
if (lmp->update->ntimestep % fix->peratom_freq) { if (lmp->update->ntimestep % fix->peratom_freq) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): fix {} not computed at compatible time",
lmp->error->all(FLERR,"lammps_gather_concat: fix not computed at compatible time"); fixid);
return; return;
} }
@ -4227,21 +4248,21 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
if (vptr==nullptr && utils::strmatch(name,"^c_")) { if (vptr==nullptr && utils::strmatch(name,"^c_")) {
auto compute = lmp->modify->get_compute_by_id(&name[2]); const char *compid = name + 2;
auto compute = lmp->modify->get_compute_by_id(compid);
if (!compute) { if (!compute) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): unknown compute id {}", compid);
lmp->error->warning(FLERR,"lammps_gather_concat: unknown compute id");
return; return;
} }
if (compute->peratom_flag == 0) { if (compute->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): compute {} does not return peratom data",
lmp->error->warning(FLERR,"lammps_gather_concat: compute does not return peratom data"); compid);
return; return;
} }
if ((count > 1) && (compute->size_peratom_cols != count)) { if ((count > 1) && (compute->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for compute {}",
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for compute"); compid);
return; return;
} }
@ -4257,28 +4278,26 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
if ((vptr==nullptr) && utils::strmatch(name,"^[id]2?_")) { if ((vptr==nullptr) && utils::strmatch(name,"^[id]2?_")) {
int idx,icol; int idx,icol;
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); const char *propid;
else idx = lmp->atom->find_custom(&name[3],ltype,icol); if (utils::strmatch(name,"^[id]_")) propid = name + 2;
else propid = name + 3;
idx = lmp->atom->find_custom(propid,ltype,icol);
if (idx < 0) { if (idx < 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): unknown property/atom id {}", propid);
lmp->error->warning(FLERR,"lammps_gather_concat: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} type", propid);
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom type");
return; return;
} }
if ((count == 1) && (icol != 0)) { if ((count == 1) && (icol != 0)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count");
return; return;
} }
if ((count > 1) && (icol != count)) { if ((count > 1) && (icol != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count");
return; return;
} }
@ -4294,8 +4313,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
// no match // no match
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_concat(): undefined property {}", name);
lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name");
return; return;
} }
@ -4405,7 +4423,14 @@ look like {x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2], x[210]
:math:`\dots`}); *ids* must be provided by the user with length *ndata*, and *data* must be :math:`\dots`}); *ids* must be provided by the user with length *ndata*, and *data* must be
pre-allocated by the caller to length (*count*\ :math:`{}\times{}`\ *ndata*). pre-allocated by the caller to length (*count*\ :math:`{}\times{}`\ *ndata*).
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and an :doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -4471,8 +4496,7 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all (FLERR,"lammps_gather_subset(): atom IDs must be enabled and mapped");
lmp->error->warning(FLERR,"Library error in lammps_gather_subset");
return; return;
} }
@ -4481,26 +4505,24 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
// fix // fix
if (vptr==nullptr && utils::strmatch(name,"^f_")) { if (vptr==nullptr && utils::strmatch(name,"^f_")) {
const char *fixid = name + 2;
auto fix = lmp->modify->get_fix_by_id(&name[2]); auto fix = lmp->modify->get_fix_by_id(fixid);
if (!fix) { if (!fix) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): unknown fix id {}", fixid);
lmp->error->warning(FLERR,"lammps_gather_subset: unknown fix id");
return; return;
} }
if (fix->peratom_flag == 0) { if (fix->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): fix {} does not return peratom data", fixid);
lmp->error->warning(FLERR,"lammps_gather_subset: fix does not return peratom data");
return; return;
} }
if ((count > 1) && (fix->size_peratom_cols != count)) { if ((count > 1) && (fix->size_peratom_cols != count)) {
lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for fix"); lmp->error->all(FLERR,"lammps_gather_subset(): count != values peratom for fix {}", fixid);
return; return;
} }
if (lmp->update->ntimestep % fix->peratom_freq) { if (lmp->update->ntimestep % fix->peratom_freq) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): fix {} not computed at compatible time", fixid);
lmp->error->all(FLERR,"lammps_gather_subset: fix not computed at compatible time");
return; return;
} }
@ -4511,22 +4533,21 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
// compute // compute
if (vptr==nullptr && utils::strmatch(name,"^c_")) { if (vptr==nullptr && utils::strmatch(name,"^c_")) {
const char *compid = name + 2;
auto compute = lmp->modify->get_compute_by_id(&name[2]); auto compute = lmp->modify->get_compute_by_id(compid);
if (!compute) { if (!compute) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): unknown compute id {}", compid);
lmp->error->warning(FLERR,"lammps_gather_subset: unknown compute id");
return; return;
} }
if (compute->peratom_flag == 0) { if (compute->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): compute {} does not return peratom data",
lmp->error->warning(FLERR,"lammps_gather_subset: compute does not return peratom data"); compid);
return; return;
} }
if ((count > 1) && (compute->size_peratom_cols != count)) { if ((count > 1) && (compute->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): count != values peratom for compute {}",
lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for compute"); compid);
return; return;
} }
@ -4542,28 +4563,26 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
int idx,icol; int idx,icol;
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); const char *propid;
else idx = lmp->atom->find_custom(&name[3],ltype,icol); if (utils::strmatch(name,"^[id]_")) propid = name + 2;
else propid = name + 3;
idx = lmp->atom->find_custom(propid,ltype,icol);
if (idx < 0) { if (idx < 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): unknown property/atom id {}", propid);
lmp->error->warning(FLERR,"lammps_gather_subset: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} type", propid);
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom type");
return; return;
} }
if (count == 1 && icol != 0) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count");
return; return;
} }
if (count > 1 && icol != count) { if (count > 1 && icol != count) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count");
return; return;
} }
@ -4579,8 +4598,7 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
// no match // no match
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_gather_subset(): undefined property {}", name);
lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name");
return; return;
} }
@ -4688,7 +4706,15 @@ The *data* array needs to be ordered in groups of *count* values, sorted by atom
*name* is *x* and *count* = 3, then *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], *name* is *x* and *count* = 3, then *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1],
x[1][2], x[2][0], :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). x[1][2], x[2][0], :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*).
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined, must be consecutive, and an
:doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -4751,8 +4777,7 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): atom IDs must be defined, consecutive, and mapped");
lmp->error->warning(FLERR,"Library error in lammps_scatter");
return; return;
} }
@ -4762,22 +4787,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
// fix // fix
if (vptr==nullptr && utils::strmatch(name,"^f_")) { if (vptr==nullptr && utils::strmatch(name,"^f_")) {
const char *fixid = name + 2;
auto fix = lmp->modify->get_fix_by_id(&name[2]); auto fix = lmp->modify->get_fix_by_id(fixid);
if (!fix) { if (!fix) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): unknown fix id {}", fixid);
lmp->error->warning(FLERR,"lammps_scatter: unknown fix id");
return; return;
} }
if (fix->peratom_flag == 0) { if (fix->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): fix {} does not return peratom data", fixid);
lmp->error->warning(FLERR,"lammps_scatter: fix does not return peratom data");
return; return;
} }
if ((count > 1) && (fix->size_peratom_cols != count)) { if ((count > 1) && (fix->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for fix {}", fixid);
lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for fix");
return; return;
} }
@ -4788,22 +4810,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
// compute // compute
if (vptr==nullptr && utils::strmatch(name,"^c_")) { if (vptr==nullptr && utils::strmatch(name,"^c_")) {
const char *compid = name + 2;
auto compute = lmp->modify->get_compute_by_id(&name[2]); auto compute = lmp->modify->get_compute_by_id(compid);
if (!compute) { if (!compute) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): unknown compute id {}",compid);
lmp->error->warning(FLERR,"lammps_scatter: unknown compute id");
return; return;
} }
if (compute->peratom_flag == 0) { if (compute->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): compute {} does not return peratom data", compid);
lmp->error->warning(FLERR,"lammps_scatter: compute does not return peratom data");
return; return;
} }
if ((count > 1) && (compute->size_peratom_cols != count)) { if ((count > 1) && (compute->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for compute {}", compid);
lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for compute");
return; return;
} }
@ -4819,28 +4838,26 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
int idx,icol; int idx,icol;
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); const char *propid;
else idx = lmp->atom->find_custom(&name[3],ltype,icol); if (utils::strmatch(name,"^[id]_")) propid = name + 2;
else propid = name + 3;
idx = lmp->atom->find_custom(propid,ltype,icol);
if (idx < 0) { if (idx < 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): unknown property/atom id {}", propid);
lmp->error->warning(FLERR,"lammps_scatter: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} type", propid);
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom type");
return; return;
} }
if (count == 1 && icol != 0) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
return; return;
} }
if (count > 1 && icol != count) { if (count > 1 && icol != count) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
return; return;
} }
@ -4856,8 +4873,7 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
// no match // no match
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter(): unknown property {}", name);
lmp->error->warning(FLERR,"lammps_scatter: unknown property name");
return; return;
} }
@ -4938,7 +4954,14 @@ to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2],
x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would
be {1, 100, 57}. be {1, 100, 57}.
This function is not compatible with ``-DLAMMPS_BIGBIG``. .. admonition:: Restrictions
:class: warning
This function is not compatible with ``-DLAMMPS_BIGBIG``.
Atom IDs must be defined and an :doc:`atom map must be enabled <atom_modify>`
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
\endverbatim \endverbatim
* *
@ -4979,8 +5002,8 @@ This function is not compatible with ``-DLAMMPS_BIGBIG``.
loop over Ndata, if I own atom ID, set its values from data loop over Ndata, if I own atom ID, set its values from data
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void lammps_scatter_subset(void *handle, const char *name,int type, int count, void lammps_scatter_subset(void *handle, const char *name,int type, int count, int ndata,
int ndata, int *ids, void *data) int *ids, void *data)
{ {
auto lmp = (LAMMPS *) handle; auto lmp = (LAMMPS *) handle;
@ -5001,8 +5024,7 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1; if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): atom-IDs must be defined and mapped");
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset");
return; return;
} }
@ -5011,22 +5033,19 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
// fix // fix
if (vptr==nullptr && utils::strmatch(name,"^f_")) { if (vptr==nullptr && utils::strmatch(name,"^f_")) {
const char *fixid = name + 2;
auto fix = lmp->modify->get_fix_by_id(&name[2]); auto fix = lmp->modify->get_fix_by_id(fixid);
if (!fix) { if (!fix) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): unknown fix id {}", fixid);
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown fix id");
return; return;
} }
if (fix->peratom_flag == 0) { if (fix->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): fix {} does not return peratom data", fixid);
lmp->error->warning(FLERR,"lammps_scatter_subset: fix does not return peratom data");
return; return;
} }
if ((count > 1) && (fix->size_peratom_cols != count)) { if ((count > 1) && (fix->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for fix {}", fixid);
lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for fix");
return; return;
} }
@ -5037,22 +5056,21 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
// compute // compute
if (vptr==nullptr && utils::strmatch(name,"^c_")) { if (vptr==nullptr && utils::strmatch(name,"^c_")) {
const char *compid = name + 2;
auto compute = lmp->modify->get_compute_by_id(&name[2]); auto compute = lmp->modify->get_compute_by_id(compid);
if (!compute) { if (!compute) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): unknown compute id {}", compid);
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown compute id");
return; return;
} }
if (compute->peratom_flag == 0) { if (compute->peratom_flag == 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): compute {} does not return peratom data",
lmp->error->warning(FLERR,"lammps_scatter_subset: compute does not return peratom data"); compid);
return; return;
} }
if ((count > 1) && (compute->size_peratom_cols != count)) { if ((count > 1) && (compute->size_peratom_cols != count)) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for compute {}",
lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for compute"); compid);
return; return;
} }
@ -5068,28 +5086,26 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) { if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
int idx,icol; int idx,icol;
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol); const char *propid;
else idx = lmp->atom->find_custom(&name[3],ltype,icol); if (utils::strmatch(name,"^[id]_")) propid = name + 2;
else propid = name + 3;
idx = lmp->atom->find_custom(propid,ltype,icol);
if (idx < 0) { if (idx < 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property/atom id {}", propid);
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} type", propid);
lmp->error->warning(FLERR,"lammps_scatter_subset: mismatch property/atom type");
return; return;
} }
if (count == 1 && icol != 0) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return; return;
} }
if (count > 1 && icol != count) { if (count > 1 && icol != count) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid);
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return; return;
} }
@ -5105,9 +5121,7 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
// no match // no match
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property {}", name);
lmp->error->warning(FLERR,"lammps_scatter_atoms_subset: "
"unknown property name");
return; return;
} }
@ -5246,7 +5260,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type,
// error if box does not exist or tags not defined // error if box does not exist or tags not defined
int flag = 0; int flag = 0;
std::string msg("Failure in lammps_create_atoms: "); std::string msg("Failure in lammps_create_atoms(): ");
if (lmp->domain->box_exist == 0) { if (lmp->domain->box_exist == 0) {
flag = 1; flag = 1;
msg += "trying to create atoms before before simulation box is defined"; msg += "trying to create atoms before before simulation box is defined";
@ -5257,7 +5271,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type,
} }
if (flag) { if (flag) {
if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); lmp->error->all(FLERR, msg);
return -1; return -1;
} }