Merge pull request #4134 from akohlmey/collected-small-changes
Collected small changes and bugfixes
This commit is contained in:
Axel Kohlmeyer
@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number
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Ntypes for each interaction is "locked in" when the simulation box
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is created.
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A recent addition to LAMMPS is the option to use strings - referred
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to as type labels - as an alternative. Using type labels instead of
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A recent addition to LAMMPS is the option to use strings - referred to
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as type labels - as an alternative. Using type labels instead of
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numeric types can be advantageous in various scenarios. For example,
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type labels can make inputs more readable and generic (i.e. usable through
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the :doc:`include command <include>` for different systems with different
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numerical values assigned to types. This generality also applies to
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other inputs like data files read by :doc:`read_data <read_data>` or
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molecule template files read by the :doc:`molecule <molecule>`
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command. See below for a list of other commands that can use
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type labels in different ways.
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type labels can make inputs more readable and generic (i.e. usable
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through the :doc:`include command <include>` for different systems with
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different numerical values assigned to types. This generality also
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applies to other inputs like data files read by :doc:`read_data
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<read_data>` or molecule template files read by the :doc:`molecule
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<molecule>` command. A discussion of the current type label support can
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be found in :ref:`(Gissinger) <Typelabel24>`. See below for a list of
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other commands that can use type labels in different ways.
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LAMMPS will *internally* continue to use numeric types, which means
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that many previous restrictions still apply. For example, the total
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@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates
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for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
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type labels, and results in templates that can be used without
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modification in multiple simulations or different systems.
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-----------
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.. _Typelabel24:
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**(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).
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@ -29,7 +29,7 @@ General features
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* spatial decomposition of simulation domain for MPI parallelism
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* particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
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* GPLv2 licensed open-source distribution
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* highly portable C++-11
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* highly portable C++-11 (optional packages may require C++17)
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* modular code with most functionality in optional packages
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* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
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* other libraries are optional and only required for specific packages
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@ -81,7 +81,7 @@ commands)
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* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
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* charged pairwise potentials: Coulombic, point-dipole
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* 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
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* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN
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* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP
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* interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
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* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
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* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`
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@ -54,8 +54,21 @@ like this:
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x[3] = x coord of atom with ID 2
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...
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x[n3-1] = z coord of atom with ID natoms
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lmp.scatter_atoms("x",1,3,x)
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lmp.scatter_atoms("x", 1, 3, x)
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The coordinates can also be provided as arguments to the initializer of x:
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.. code-block:: python
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from ctypes import c_double
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natoms = 2
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n3 = 3*natoms
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# init in constructor
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x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0)
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lmp.scatter_atoms("x", 1, 3, x)
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# or using a list
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coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0]
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x = (c_double*len(coords))(*coords)
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Alternatively, you can just change values in the vector returned by
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the gather methods, since they are also ctypes vectors.
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@ -43,7 +43,8 @@ The label map can also be defined by the :doc:`read_data <read_data>`
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command when it reads these sections in a data file: Atom Type Labels,
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Bond Type Labels, etc. See the :doc:`Howto type labels
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<Howto_type_labels>` doc page for a general discussion of how type
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labels can be used.
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labels can be used. See :ref:`(Gissinger) <Typelabel>` for a discussion
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of the type label implementation in LAMMPS and its uses.
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Valid type labels can contain any alphanumeric character, but must not
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start with a number, a '#', or a '*' character. They can contain other
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@ -98,3 +99,9 @@ Default
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"""""""
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none
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-----------
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.. _Typelabel:
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**(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).
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@ -140,6 +140,21 @@ The OpenKIM Project at
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provides EAM potentials that can be used directly in LAMMPS with the
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:doc:`kim command <kim_commands>` interface.
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.. warning::
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The EAM potential files tabulate the embedding energy as a function
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of the local electron density :math:`\rho`. When atoms get too
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close, this electron density may exceed the range for which the
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embedding energy was tabulated for. To avoid crashes, LAMMPS will
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assume a linearly increasing embedding energy for electron densities
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beyond the maximum tabulated value. LAMMPS will print a warning when
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this happens. It may be acceptable at the beginning of an
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equilibration (e.g. when using randomized coordinates) but would be a
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big concern for accuracy if it happens during production runs. The
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EAM potential file triggering the warning during production is thus
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not a good choice, and the EAM model in general not likely a good
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model for the kind of system under investigation.
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----------
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For style *eam*, potential values are read from a file that is in the
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@ -492,6 +492,7 @@ ChiralIDs
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chirality
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Cho
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Chodera
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Choi
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ChooseOffset
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chris
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Christoph
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@ -17,9 +17,9 @@ rho_e, electrons/volume units
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D_e, length^2/time units
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20000
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gamma_p, mass/time units
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39.235
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gamma_s, mass/time units
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24.443
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gamma_s, mass/time units
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39.235
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v_0, length/time units
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79.76
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I_0, energy/(time*length^2) units
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@ -1,4 +1,5 @@
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LAMMPS (28 Mar 2023 - Development)
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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boundary p p p
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@ -13,7 +14,7 @@ mass 1 28.0855
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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
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Created 8000 atoms
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using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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create_atoms CPU = 0.002 seconds
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create_atoms CPU = 0.001 seconds
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pair_style sw
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pair_coeff * * Si.sw Si
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@ -79,30 +80,30 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
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0 0 -34692.79996100604 -52.79390940511979 0
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100 2.004897156140836 -34690.27961013186 -55.3499730543189 0.01301140393178352
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200 2.837118035232607 -34687.74741132015 -57.93445748841876 0.02696025968760173
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300 4.263087164947482 -34684.98084093686 -60.75945453846793 0.02175636603841567
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400 5.568003854939066 -34682.25271040963 -63.56896518300499 0.03000618483472749
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500 6.225602451570786 -34679.49948952029 -66.40897551884574 0.02768827702656703
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600 7.608847536264781 -34676.69728436362 -69.32060611557282 0.05579466731854091
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700 9.049471241531297 -34674.00093206036 -72.10055094219462 0.004335980559879032
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800 9.826796099683211 -34671.27720242751 -74.95010610862134 0.02371649678091515
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900 11.8609224958918 -34668.35091308811 -77.98544170794545 0.004658649791374908
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1000 13.88037467640968 -34665.35025858006 -81.16445160194111 0.07684078334464743
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Loop time of 2.48942 on 1 procs for 1000 steps with 8000 atoms
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100 1.255921182965094 -34691.22889627319 -54.38067722556279 0.004868249873095404
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200 1.858362347834853 -34689.5405389424 -56.09419523244324 0.01649190747838086
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300 2.581575104085017 -34687.9650112138 -57.69350558275053 0.01683584513983131
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400 3.47533128765632 -34686.2796683925 -59.40465113478642 0.005727647825729662
|
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500 4.080137293185865 -34684.25857873315 -61.46449138661911 0.005828121949923951
|
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600 4.816104423494803 -34682.51412688349 -63.25804498666959 0.02397283419020746
|
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700 5.937291156573137 -34680.64941595491 -65.17152689673857 0.02604017750117964
|
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800 6.487028971399661 -34678.87151939966 -66.99420300650799 0.009720189851817886
|
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900 7.461479797687167 -34677.29259652842 -68.63442522233655 0.02576822683306545
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1000 8.696444335455215 -34675.39247806347 -70.59264558122587 0.0147252863003017
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Loop time of 5.11497 on 1 procs for 1000 steps with 8000 atoms
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Performance: 3.471 ns/day, 6.915 hours/ns, 401.700 timesteps/s, 3.214 Matom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 1.689 ns/day, 14.208 hours/ns, 195.505 timesteps/s, 1.564 Matom-step/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.126 | 2.126 | 2.126 | 0.0 | 85.40
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Pair | 4.3498 | 4.3498 | 4.3498 | 0.0 | 85.04
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.016147 | 0.016147 | 0.016147 | 0.0 | 0.65
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Output | 0.0013116 | 0.0013116 | 0.0013116 | 0.0 | 0.05
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Modify | 0.33864 | 0.33864 | 0.33864 | 0.0 | 13.60
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Other | | 0.007318 | | | 0.29
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Comm | 0.037981 | 0.037981 | 0.037981 | 0.0 | 0.74
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Output | 0.0025641 | 0.0025641 | 0.0025641 | 0.0 | 0.05
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Modify | 0.71279 | 0.71279 | 0.71279 | 0.0 | 13.94
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Other | | 0.01179 | | | 0.23
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Nlocal: 8000 ave 8000 max 8000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -117,4 +118,4 @@ Total # of neighbors = 272000
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Ave neighs/atom = 34
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:02
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Total wall time: 0:00:05
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@ -1,5 +1,5 @@
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LAMMPS (28 Mar 2023 - Development)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:531)
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-394-g03ab36a37d)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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boundary p p p
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@ -14,7 +14,7 @@ mass 1 28.0855
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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
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Created 8000 atoms
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using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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create_atoms CPU = 0.001 seconds
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create_atoms CPU = 0.002 seconds
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pair_style sw
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pair_coeff * * Si.sw Si
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@ -80,30 +80,30 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes
|
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
|
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0 0 -34692.79996100361 -52.79390940511979 0
|
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100 1.852689977101411 -34690.49204900486 -55.14271612882064 0.02726188676577098
|
||||
200 2.735750477179192 -34688.11139028054 -57.57110998717798 0.03387986355513584
|
||||
300 3.931848271449558 -34685.54667417785 -60.18684521127231 0.02261256315262403
|
||||
400 5.462009198576365 -34682.74455105668 -63.05420336037233 0.002402241637719578
|
||||
500 6.267811692893873 -34679.96493887379 -65.93304222280051 0.02448378880218699
|
||||
600 7.21148216150661 -34677.41455784726 -68.58391420045926 0.04114045759945374
|
||||
700 8.84660534187052 -34674.40610468235 -71.68798344296859 0.02372984027434538
|
||||
800 10.1748456457686 -34671.08749605772 -75.11943618276216 0.007538225788030307
|
||||
900 11.27479036162859 -34668.4118066423 -77.92921692176756 0.02537529314475071
|
||||
1000 13.26881394868076 -34665.56617589539 -80.91544540266317 0.03112665440209921
|
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Loop time of 0.995347 on 4 procs for 1000 steps with 8000 atoms
|
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100 1.20337355884597 -34691.30677367127 -54.30747356568817 0.01557346850238741
|
||||
200 1.709631732825883 -34689.83859944795 -55.7982356998371 0.02508386983502213
|
||||
300 2.488524478071323 -34688.26307995134 -57.3977272154369 0.02664346353990833
|
||||
400 3.38535890366476 -34686.51395648598 -59.17547816947624 0.02164200191836632
|
||||
500 3.838163353802383 -34684.79466673204 -60.92228950760077 0.005860499116196545
|
||||
600 4.675913079756001 -34683.03448988724 -62.72423959707044 0.0106700119158327
|
||||
700 5.637185532827328 -34681.25888274477 -64.5491928842093 0.01568536325219336
|
||||
800 6.316986413957468 -34679.29231578312 -66.57005328290739 0.02035373879569394
|
||||
900 7.211479047111087 -34677.61236020172 -68.30976417874265 0.03239086895076279
|
||||
1000 8.431725106300505 -34675.81097854214 -70.161139196977 0.01219385884660358
|
||||
Loop time of 1.73439 on 4 procs for 1000 steps with 8000 atoms
|
||||
|
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Performance: 8.680 ns/day, 2.765 hours/ns, 1004.675 timesteps/s, 8.037 Matom-step/s
|
||||
97.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 4.982 ns/day, 4.818 hours/ns, 576.572 timesteps/s, 4.613 Matom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
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MPI task timing breakdown:
|
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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
|
||||
Comm | 0.041606 | 0.048314 | 0.056589 | 2.9 | 4.85
|
||||
Output | 0.0014609 | 0.0014742 | 0.0014968 | 0.0 | 0.15
|
||||
Modify | 0.27934 | 0.28016 | 0.28089 | 0.1 | 28.15
|
||||
Other | | 0.003798 | | | 0.38
|
||||
Comm | 0.068488 | 0.082304 | 0.094797 | 4.1 | 4.75
|
||||
Output | 0.0024745 | 0.0025221 | 0.0025705 | 0.1 | 0.15
|
||||
Modify | 0.50194 | 0.50329 | 0.50522 | 0.2 | 29.02
|
||||
Other | | 0.007117 | | | 0.41
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
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||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -192,11 +192,23 @@ class Atom(object):
|
||||
@property
|
||||
def mass(self):
|
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"""
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Return the atom mass
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||||
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
|
||||
"""
|
||||
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
|
||||
def radius(self):
|
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|
||||
@ -32,8 +32,8 @@ using namespace LAMMPS_NS;
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairPedone::PairPedone(LAMMPS *lmp) :
|
||||
Pair(lmp), d0(nullptr), alpha(nullptr), r0(nullptr), c0(nullptr), pedone1(nullptr),
|
||||
pedone2(nullptr)
|
||||
Pair(lmp), cut(nullptr), d0(nullptr), alpha(nullptr), r0(nullptr), c0(nullptr),
|
||||
pedone1(nullptr), pedone2(nullptr), offset(nullptr)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
@ -234,7 +234,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
|
||||
const int istride = fc.rhor_istride();
|
||||
const int jstride = fc.rhor_jstride();
|
||||
const int fstride = fc.frho_stride();
|
||||
|
||||
int beyond_rhomax = 0;
|
||||
{
|
||||
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
|
||||
*timer_compute = MIC_Wtime();
|
||||
@ -453,7 +453,10 @@ void PairEAMIntel::eval(const int offload, const int vflag,
|
||||
if (EFLAG) {
|
||||
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;
|
||||
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) {
|
||||
const int ptr_off=itype*ntypes + itype;
|
||||
oscale = scale_f[ptr_off];
|
||||
@ -653,6 +656,16 @@ void PairEAMIntel::eval(const int offload, const int vflag,
|
||||
else
|
||||
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)
|
||||
fix->add_result_array(f_start, ev_global, offload, eatom, 0, vflag);
|
||||
else
|
||||
@ -849,4 +862,3 @@ void PairEAMIntel::unpack_forward_comm(int n, int first, double *buf,
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) fp_f[i] = buf[m++];
|
||||
}
|
||||
|
||||
|
||||
@ -148,6 +148,8 @@ void PairEAM::compute(int eflag, int vflag)
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
int beyond_rhomax = 0;
|
||||
|
||||
// grow energy and fp arrays if necessary
|
||||
// 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];
|
||||
if (eflag) {
|
||||
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]];
|
||||
if (eflag_global) eng_vdwl += 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();
|
||||
}
|
||||
|
||||
@ -424,6 +439,8 @@ void PairEAM::init_style()
|
||||
|
||||
neighbor->add_request(this);
|
||||
embedstep = -1;
|
||||
|
||||
exceeded_rhomax = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -68,6 +68,9 @@ class PairEAM : public Pair {
|
||||
double **scale;
|
||||
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
|
||||
|
||||
double *rho, *fp;
|
||||
|
||||
@ -17,6 +17,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
@ -102,6 +103,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
double *coeff;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
int beyond_rhomax = 0;
|
||||
evdwl = 0.0;
|
||||
|
||||
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];
|
||||
if (EFLAG) {
|
||||
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);
|
||||
}
|
||||
}
|
||||
@ -298,6 +303,16 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
f[i].y += fytmp;
|
||||
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");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -23,6 +23,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.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 ntypes2 = ntypes * ntypes;
|
||||
int beyond_rhomax = 0;
|
||||
|
||||
auto *_noalias fast_alpha =
|
||||
(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];
|
||||
if (EFLAG) {
|
||||
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]];
|
||||
if (eflag_global) eng_vdwl += 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);
|
||||
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();
|
||||
}
|
||||
|
||||
430
src/library.cpp
430
src/library.cpp
@ -527,7 +527,7 @@ void lammps_file(void *handle, const char *filename)
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
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
|
||||
lmp->input->file(filename);
|
||||
}
|
||||
@ -564,8 +564,7 @@ char *lammps_command(void *handle, const char *cmd)
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
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 command during a run is not allowed.");
|
||||
else
|
||||
result = lmp->input->one(cmd);
|
||||
}
|
||||
@ -641,7 +640,7 @@ void lammps_commands_string(void *handle, const char *str)
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
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;
|
||||
@ -949,9 +948,9 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
// do nothing if box does not yet exist
|
||||
if ((lmp->domain->box_exist == 0)
|
||||
&& (lmp->comm->me == 0)) {
|
||||
lmp->error->warning(FLERR,"Calling lammps_extract_box without a box");
|
||||
if (lmp->domain->box_exist == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR, "Call to lammps_extract_box() without a box ignored");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -1011,12 +1010,12 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
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
|
||||
if (lmp->domain->box_exist == 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;
|
||||
}
|
||||
|
||||
@ -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`,
|
||||
: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
|
||||
*
|
||||
@ -2650,8 +2656,7 @@ This function is not compatible with ``-DLAMMPS_BIGBIG``.
|
||||
Allreduce to sum vector into data across all procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void lammps_gather_atoms(void *handle, const char *name, int type, int count,
|
||||
void *data)
|
||||
void lammps_gather_atoms(void *handle, const char *name, int type, int count, void *data)
|
||||
{
|
||||
auto lmp = (LAMMPS *) handle;
|
||||
|
||||
@ -2671,8 +2676,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count,
|
||||
flag = 1;
|
||||
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms(): Atom-IDs must exist and be consecutive");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -2680,8 +2684,7 @@ void lammps_gather_atoms(void *handle, const char *name, int type, int count,
|
||||
|
||||
void *vptr = lmp->atom->extract(name);
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
|
||||
lmp->error->all(FLERR, "lammps_gather_atoms(): unknown property {}", name);
|
||||
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);
|
||||
lmp->memory->destroy(copy);
|
||||
} else {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_atoms: unsupported data type");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms(): unsupported data type");
|
||||
return;
|
||||
}
|
||||
#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],
|
||||
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
|
||||
queried by :cpp:func:`lammps_get_natoms`,
|
||||
:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`.
|
||||
queried by :cpp:func:`lammps_get_natoms`, :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.
|
||||
|
||||
The total number of atoms must not be more than 2147483647 (max 32-bit signed int).
|
||||
|
||||
\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->natoms > MAXSMALLINT) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms_concat(): Atom-IDs must exist");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -2837,8 +2845,7 @@ void lammps_gather_atoms_concat(void *handle, const char *name, int type,
|
||||
|
||||
void *vptr = lmp->atom->extract(name);
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms_concat(): unknown property {}", name);
|
||||
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
|
||||
(*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
|
||||
*
|
||||
@ -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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms_subset: atoms must have mappable ids");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms_subset(): Atom-IDs must exist and be mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
void *vptr = lmp->atom->extract(name);
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_atoms_subset: "
|
||||
"unknown property name");
|
||||
lmp->error->all(FLERR,"lammps_gather_atoms_subset(): unknown property {}", name);
|
||||
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],
|
||||
: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
|
||||
*
|
||||
@ -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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms: ids must exist, be consecutive, and be mapped");
|
||||
lmp->error->all(FLERR,"lammps_scatter_atoms(): "
|
||||
"Atom-IDs must exist, be consecutive, and be mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -3161,9 +3180,7 @@ void lammps_scatter_atoms(void *handle, const char *name, int type, int count,
|
||||
|
||||
void *vptr = lmp->atom->extract(name);
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,
|
||||
"lammps_scatter_atoms: unknown property name");
|
||||
lmp->error->all(FLERR, "lammps_scatter_atoms(): unknown property {}", name);
|
||||
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
|
||||
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
|
||||
*
|
||||
@ -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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset: atoms must have mapped ids");
|
||||
lmp->error->all(FLERR,"lammps_scatter_atoms_subset(): Atom-IDs must exist and be mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
void *vptr = lmp->atom->extract(name);
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,
|
||||
"lammps_scatter_atoms_subset: unknown property name");
|
||||
lmp->error->all(FLERR, "lammps_scatter_atoms_subset(): unknown property {}", name);
|
||||
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
|
||||
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
|
||||
*
|
||||
@ -3899,7 +3927,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
#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
|
||||
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;
|
||||
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather");
|
||||
lmp->error->all(FLERR,"lammps_gather(): Atom-IDs must exist, and be consecutive");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -3921,28 +3948,25 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
|
||||
// fix
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: unknown fix id");
|
||||
lmp->error->all(FLERR,"lammps_gather(): unknown fix id {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (fix->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: fix does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather(): fix {} does not return peratom data", fixid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (fix->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: count != values peratom for fix");
|
||||
lmp->error->all(FLERR,"lammps_gather: count != values peratom for fix {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (lmp->update->ntimestep % fix->peratom_freq) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->all(FLERR,"lammps_gather: fix not computed at compatible time");
|
||||
lmp->error->all(FLERR,"lammps_gather: fix {} not computed at compatible time", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -3953,22 +3977,19 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
|
||||
// compute
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: unknown compute id");
|
||||
lmp->error->all(FLERR,"lammps_gather(): unknown compute id {}", compid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (compute->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: compute does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather(): compute {} does not return peratom data", compid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (compute->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: count != values peratom for compute");
|
||||
lmp->error->all(FLERR,"lammps_gather(): count != values peratom for compute {}", compid);
|
||||
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?_")) {
|
||||
|
||||
int idx,icol;
|
||||
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol);
|
||||
else idx = lmp->atom->find_custom(&name[3],ltype,icol);
|
||||
const char *propid;
|
||||
if (utils::strmatch(name,"^[id]_")) propid = name+2;
|
||||
else propid = name+3;
|
||||
idx = lmp->atom->find_custom(propid,ltype,icol);
|
||||
|
||||
if (idx < 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: unknown property/atom id");
|
||||
lmp->error->all(FLERR,"lammps_gather(): unknown property/atom id {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (ltype != type) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom type");
|
||||
lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom type for {}", propid);
|
||||
return;
|
||||
}
|
||||
if ((count == 1) && (icol != 0)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (icol != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather(): mismatch property/atom count for {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4021,8 +4040,7 @@ void lammps_gather(void *handle, const char *name, int type, int count, void *da
|
||||
// no match
|
||||
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: undefined property name");
|
||||
lmp->error->all(FLERR,"lammps_gather(): undefined property {}", name);
|
||||
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_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
|
||||
*
|
||||
@ -4173,8 +4198,8 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
lmp->error->all(FLERR,"Library function lammps_gather_concat"
|
||||
" not compatible with -DLAMMPS_BIGBIG");
|
||||
lmp->error->all(FLERR,"Library function lammps_gather_concat()"
|
||||
" is not compatible with -DLAMMPS_BIGBIG");
|
||||
#else
|
||||
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->natoms > MAXSMALLINT) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather_concat");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): atom-IDs must exist");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4195,27 +4219,24 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
|
||||
// fix
|
||||
|
||||
if (vptr==nullptr && utils::strmatch(name,"^f_")) {
|
||||
|
||||
auto fix = lmp->modify->get_fix_by_id(&name[2]);
|
||||
const char *fixid = name+2;
|
||||
auto fix = lmp->modify->get_fix_by_id(fixid);
|
||||
if (!fix) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: unknown fix id");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): unknown fix id {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (fix->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: fix does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): fix {} does not return peratom data", fixid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (fix->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for fix");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for fix {}", fixid);
|
||||
return;
|
||||
}
|
||||
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;
|
||||
}
|
||||
|
||||
@ -4227,21 +4248,21 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: unknown compute id");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): unknown compute id {}", compid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (compute->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: compute does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): compute {} does not return peratom data",
|
||||
compid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (compute->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for compute");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): count != values peratom for compute {}",
|
||||
compid);
|
||||
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?_")) {
|
||||
|
||||
int idx,icol;
|
||||
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol);
|
||||
else idx = lmp->atom->find_custom(&name[3],ltype,icol);
|
||||
const char *propid;
|
||||
if (utils::strmatch(name,"^[id]_")) propid = name + 2;
|
||||
else propid = name + 3;
|
||||
idx = lmp->atom->find_custom(propid,ltype,icol);
|
||||
|
||||
if (idx < 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: unknown property/atom id");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): unknown property/atom id {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (ltype != type) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom type");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} type", propid);
|
||||
return;
|
||||
}
|
||||
if ((count == 1) && (icol != 0)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (icol != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4294,8 +4313,7 @@ void lammps_gather_concat(void *handle, const char *name, int type, int count,
|
||||
// no match
|
||||
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name");
|
||||
lmp->error->all(FLERR,"lammps_gather_concat(): undefined property {}", name);
|
||||
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
|
||||
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
|
||||
*
|
||||
@ -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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_gather_subset");
|
||||
lmp->error->all (FLERR,"lammps_gather_subset(): atom IDs must be enabled and mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4481,26 +4505,24 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
|
||||
// fix
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: unknown fix id");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): unknown fix id {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (fix->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: fix does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): fix {} does not return peratom data", fixid);
|
||||
return;
|
||||
}
|
||||
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;
|
||||
}
|
||||
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");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): fix {} not computed at compatible time", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4511,22 +4533,21 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
|
||||
// compute
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: unknown compute id");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): unknown compute id {}", compid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (compute->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: compute does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): compute {} does not return peratom data",
|
||||
compid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (compute->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for compute");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): count != values peratom for compute {}",
|
||||
compid);
|
||||
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?_")) {
|
||||
|
||||
int idx,icol;
|
||||
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol);
|
||||
else idx = lmp->atom->find_custom(&name[3],ltype,icol);
|
||||
const char *propid;
|
||||
if (utils::strmatch(name,"^[id]_")) propid = name + 2;
|
||||
else propid = name + 3;
|
||||
idx = lmp->atom->find_custom(propid,ltype,icol);
|
||||
|
||||
if (idx < 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: unknown property/atom id");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): unknown property/atom id {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (ltype != type) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom type");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} type", propid);
|
||||
return;
|
||||
}
|
||||
if (count == 1 && icol != 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
if (count > 1 && icol != count) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4579,8 +4598,7 @@ void lammps_gather_subset(void *handle, const char *name, int type, int count,
|
||||
// no match
|
||||
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name");
|
||||
lmp->error->all(FLERR,"lammps_gather_subset(): undefined property {}", name);
|
||||
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],
|
||||
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
|
||||
*
|
||||
@ -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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_scatter");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): atom IDs must be defined, consecutive, and mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4762,22 +4787,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
|
||||
// fix
|
||||
|
||||
if (vptr==nullptr && utils::strmatch(name,"^f_")) {
|
||||
|
||||
auto fix = lmp->modify->get_fix_by_id(&name[2]);
|
||||
const char *fixid = name + 2;
|
||||
auto fix = lmp->modify->get_fix_by_id(fixid);
|
||||
if (!fix) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: unknown fix id");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): unknown fix id {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (fix->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: fix does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): fix {} does not return peratom data", fixid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (fix->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for fix");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for fix {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4788,22 +4810,19 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
|
||||
// compute
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: unknown compute id");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): unknown compute id {}",compid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (compute->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: compute does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): compute {} does not return peratom data", compid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (compute->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: count != values peratom for compute");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): count != values peratom for compute {}", compid);
|
||||
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?_")) {
|
||||
|
||||
int idx,icol;
|
||||
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol);
|
||||
else idx = lmp->atom->find_custom(&name[3],ltype,icol);
|
||||
const char *propid;
|
||||
if (utils::strmatch(name,"^[id]_")) propid = name + 2;
|
||||
else propid = name + 3;
|
||||
idx = lmp->atom->find_custom(propid,ltype,icol);
|
||||
|
||||
if (idx < 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: unknown property/atom id");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): unknown property/atom id {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (ltype != type) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom type");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} type", propid);
|
||||
return;
|
||||
}
|
||||
if (count == 1 && icol != 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
if (count > 1 && icol != count) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -4856,8 +4873,7 @@ void lammps_scatter(void *handle, const char *name, int type, int count,
|
||||
// no match
|
||||
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter: unknown property name");
|
||||
lmp->error->all(FLERR,"lammps_scatter(): unknown property {}", name);
|
||||
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
|
||||
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
|
||||
*
|
||||
@ -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
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void lammps_scatter_subset(void *handle, const char *name,int type, int count,
|
||||
int ndata, int *ids, void *data)
|
||||
void lammps_scatter_subset(void *handle, const char *name,int type, int count, int ndata,
|
||||
int *ids, void *data)
|
||||
{
|
||||
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->map_style == Atom::MAP_NONE) flag = 1;
|
||||
if (flag) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): atom-IDs must be defined and mapped");
|
||||
return;
|
||||
}
|
||||
|
||||
@ -5011,22 +5033,19 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
|
||||
// fix
|
||||
|
||||
if (vptr==nullptr && utils::strmatch(name,"^f_")) {
|
||||
|
||||
auto fix = lmp->modify->get_fix_by_id(&name[2]);
|
||||
const char *fixid = name + 2;
|
||||
auto fix = lmp->modify->get_fix_by_id(fixid);
|
||||
if (!fix) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown fix id");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): unknown fix id {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (fix->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: fix does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): fix {} does not return peratom data", fixid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (fix->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for fix");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for fix {}", fixid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -5037,22 +5056,21 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
|
||||
// compute
|
||||
|
||||
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 (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown compute id");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): unknown compute id {}", compid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (compute->peratom_flag == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: compute does not return peratom data");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): compute {} does not return peratom data",
|
||||
compid);
|
||||
return;
|
||||
}
|
||||
if ((count > 1) && (compute->size_peratom_cols != count)) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: count != values peratom for compute");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): count != values peratom for compute {}",
|
||||
compid);
|
||||
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?_")) {
|
||||
|
||||
int idx,icol;
|
||||
if (utils::strmatch(name,"^[id]_")) idx = lmp->atom->find_custom(&name[2],ltype,icol);
|
||||
else idx = lmp->atom->find_custom(&name[3],ltype,icol);
|
||||
const char *propid;
|
||||
if (utils::strmatch(name,"^[id]_")) propid = name + 2;
|
||||
else propid = name + 3;
|
||||
idx = lmp->atom->find_custom(propid,ltype,icol);
|
||||
|
||||
if (idx < 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown property/atom id");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property/atom id {}", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
if (ltype != type) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_subset: mismatch property/atom type");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} type", propid);
|
||||
return;
|
||||
}
|
||||
if (count == 1 && icol != 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
if (count > 1 && icol != count) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): mismatch property/atom {} count", propid);
|
||||
return;
|
||||
}
|
||||
|
||||
@ -5105,9 +5121,7 @@ void lammps_scatter_subset(void *handle, const char *name,int type, int count,
|
||||
// no match
|
||||
|
||||
if (vptr == nullptr) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"lammps_scatter_atoms_subset: "
|
||||
"unknown property name");
|
||||
lmp->error->all(FLERR,"lammps_scatter_subset(): unknown property {}", name);
|
||||
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
|
||||
|
||||
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) {
|
||||
flag = 1;
|
||||
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 (lmp->comm->me == 0) lmp->error->warning(FLERR,msg);
|
||||
lmp->error->all(FLERR, msg);
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user