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Merge branch 'master' into widom

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Axel Kohlmeyer 2020-07-15 20:46:39 -04:00
parent 581d47a10a 438346a936
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78
cmake/Modules/Packages/GPU.cmake
View File

@ -64,30 +64,41 @@ if(GPU_API STREQUAL "CUDA")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -226,30 +237,41 @@ elseif(GPU_API STREQUAL "HIP")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH} ")
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
endif()
endif()

13
doc/src/Build_extras.rst
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@ -105,10 +105,10 @@ CMake build
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_30
# default is sm_50
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_30' for HIP_PLATFORM=nvcc
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
@ -1255,6 +1255,15 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
used in tandem with the USER-INTEL package to good effect, as explained
on the :doc:`Speed intel <Speed_intel>` doc page.
When using Intel compilers version 16.0 or later is required. You can
also use the GNU or Clang compilers and they will provide performance
improvements over regular styles and USER-OMP styles, but less so than
with the Intel compilers. Please also note, that some compilers have
been found to apply memory alignment constraints incompletely or
incorrectly and thus can cause segmentation faults in otherwise correct
code when using features from the USER-INTEL package.
CMake build
^^^^^^^^^^^

3
doc/src/Commands_all.rst
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@ -101,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

51
doc/src/Howto_output.rst
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@ -3,13 +3,15 @@ Output from LAMMPS (thermo, dumps, computes, fixes, variables)
There are four basic kinds of LAMMPS output:
* :doc:`Thermodynamic output <thermo_style>`, which is a list
of quantities printed every few timesteps to the screen and logfile.
* :doc:`Thermodynamic output <thermo_style>`, which is a list of
quantities printed every few timesteps to the screen and logfile.
* :doc:`Dump files <dump>`, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency.
* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of
:doc:`variables <variable>`. Fix print can also output to the
screen.
* Certain fixes can output user-specified quantities to files:
:doc:`fix ave/time <fix_ave_time>` for time averaging,
:doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and
:doc:`fix print <fix_print>` for single-line output of
:doc:`variables <variable>`. Fix print can also output to the screen.
* :doc:`Restart files <restart>`.
A simulation prints one set of thermodynamic output and (optionally)
@ -41,7 +43,7 @@ to output and the kind of data they operate on and produce:
.. _global:
Global/per-atom/local data
---------------------------------------
--------------------------
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
@ -54,7 +56,7 @@ bond distances.
.. _scalar:
Scalar/vector/array data
-------------------------------------
------------------------
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
@ -81,10 +83,27 @@ the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
.. _disambiguation:
Disambiguation
--------------
Some computes and fixes produce data in multiple styles, e.g. a global
scalar and a per-atom vector. Usually the context in which the input
script references the data determines which style is meant. Example: if
a compute provides both a global scalar and a per-atom vector, the
former will be accessed by using ``c_ID`` in an equal-style variable,
while the latter will be accessed by using ``c_ID`` in an atom-style
variable. Note that atom-style variable formulas can also access global
scalars, but in this case it is not possible to do directly because of
the ambiguity. Instead, an equal-style variable can be defined which
accesses the global scalar, and that variable used in the atom-style
variable formula in place of ``c_ID``.
.. _thermo:
Thermodynamic output
---------------------------------
--------------------
The frequency and format of thermodynamic output is set by the
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
@ -112,7 +131,7 @@ intensive result.
.. _dump:
Dump file output
---------------------------
----------------
Dump file output is specified by the :doc:`dump <dump>` and
:doc:`dump_modify <dump_modify>` commands. There are several
@ -138,7 +157,7 @@ command.
.. _fixoutput:
Fixes that write output files
---------------------------------------------
-----------------------------
Several fixes take various quantities as input and can write output
files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
@ -192,7 +211,7 @@ from normal thermodynamic or dump file output.
.. _computeoutput:
Computes that process output quantities
-----------------------------------------------------------
---------------------------------------
The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
@ -219,7 +238,7 @@ output commands.
.. _fixprocoutput:
Fixes that process output quantities
--------------------------------------------------------
------------------------------------
The :doc:`fix vector <fix_vector>` command can create global vectors as
output from global scalars as input, accumulating them one element at
@ -244,7 +263,7 @@ The output of this fix can be used as input to other output commands.
.. _compute:
Computes that generate values to output
-----------------------------------------------------
---------------------------------------
Every :doc:`compute <compute>` in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
@ -257,7 +276,7 @@ without the word "atom" or "local" produce global values.
.. _fix:
Fixes that generate values to output
----------------------------------------------
------------------------------------
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
@ -269,7 +288,7 @@ describes them.
.. _variable:
Variables that generate values to output
-------------------------------------------------------
----------------------------------------
:doc:`Variables <variable>` defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
@ -284,7 +303,7 @@ commands described in this section.
.. _table:
Summary table of output options and data flow between commands
--------------------------------------------------------------------------
--------------------------------------------------------------
This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of

3
doc/src/Packages_details.rst
View File

@ -306,7 +306,8 @@ gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`. See
also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
**Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
(Northwestern U) while at ORNL and later. AMD HIP support by Evgeny
Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
**Install:**

4
doc/src/Speed_gpu.rst
View File

@ -50,6 +50,10 @@ but this can be overridden using the device option of the :doc:`package <package
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
platforms and devices with a suitable ICD available.
To compute and use this package in HIP mode, you have to have the AMD ROCm
software installed. Versions of ROCm older than 3.5 are currently deprecated
by AMD.
**Building LAMMPS with the GPU package:**
See the :ref:`Build extras <gpu>` doc page for

6
doc/src/Speed_intel.rst
View File

@ -138,10 +138,10 @@ For Intel Xeon Phi co-processors (Offload):
**Required hardware/software:**
When using Intel compilers version 16.0 or later is required.
In order to use offload to co-processors, an Intel Xeon Phi
co-processor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
co-processor and an Intel compiler are required.
Although any compiler can be used with the USER-INTEL package,
currently, vectorization directives are disabled by default when

3
doc/src/commands_list.rst
View File

@ -88,7 +88,8 @@ Commands
region
replicate
rerun
reset_ids
reset_atom_ids
reset_mol_ids
reset_timestep
restart
run

10
doc/src/compute_chunk_atom.rst
View File

@ -622,14 +622,16 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
**Output info:**
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
the :doc:`Howto output <Howto_output>` doc page for an overview of
This compute calculates a per-atom vector (the chunk ID), which can
be accessed by any command that uses per-atom values from a compute
as input. It also calculates a global scalar (the number of chunks),
which can be similarly accessed everywhere outside of a per-atom context.
See the :doc:`Howto output <Howto_output>` doc page for an overview of
LAMMPS output options.
The per-atom vector values are unitless chunk IDs, ranging from 1 to
*Nchunk* (inclusive) for atoms assigned to chunks, and 0 for atoms not
belonging to a chunk.
belonging to a chunk. The scalar contains the value of *Nchunk*.
Restrictions
""""""""""""

68
doc/src/compute_cluster_atom.rst
View File

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

4
doc/src/delete_atoms.rst
View File

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

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

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

116
doc/src/reset_mol_ids.rst Normal file
View File

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

5
doc/utils/sphinx-config/false_positives.txt
View File

@ -870,6 +870,7 @@ evalue
Evanseck
evdwl
Everaers
Evgeny
evirials
ewald
Ewald
@ -1484,6 +1485,7 @@ Kumar
Kuronen
Kusters
Kutta
Kuznetsov
kx
Lackmann
Ladd
@ -2030,6 +2032,7 @@ nhc
NiAlH
Nicklas
Niklasson
Nikolskiy
Nimpropertype
Ninteger
Nissila
@ -2058,6 +2061,7 @@ nodeless
nodeset
nodesets
Noehring
Noffset
noforce
Noid
nolib
@ -3203,6 +3207,7 @@ Voth
vpz
vratio
Vries
Vsevolod
Vsmall
Vstream
vtarget

44
src/KIM/kim_interactions.cpp
View File

@ -71,6 +71,7 @@
#include "universe.h"
#include "input.h"
#include "variable.h"
#include "utils.h"
#include "fix_store_kim.h"
extern "C" {
@ -149,10 +150,6 @@ void KimInteractions::do_setup(int narg, char **arg)
simulatorModel,"atom-type-num-list",atom_type_num_list.c_str());
KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
int len = atom_type_sym_list.size()+1;
char *strbuf = new char[len];
char *strword;
// validate species selection
int sim_num_species;
@ -160,28 +157,21 @@ void KimInteractions::do_setup(int narg, char **arg)
char const *sim_species;
KIM_SimulatorModel_GetNumberOfSupportedSpecies(
simulatorModel,&sim_num_species);
strcpy(strbuf,atom_type_sym_list.c_str());
strword = strtok(strbuf," \t");
while (strword) {
for (auto atom_type_sym : utils::split_words(atom_type_sym_list)) {
species_is_supported = false;
if (strcmp(strword,"NULL") == 0) continue;
if (atom_type_sym == "NULL") continue;
for (int i=0; i < sim_num_species; ++i) {
KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species);
if (strcmp(sim_species,strword) == 0)
species_is_supported = true;
if (atom_type_sym == sim_species) species_is_supported = true;
}
if (!species_is_supported) {
std::string msg("Species '");
msg += strword;
msg += "' is not supported by this KIM Simulator Model";
std::string msg = "Species '";
msg += atom_type_sym + "' is not supported by this KIM Simulator Model";
error->all(FLERR,msg);
}
strword = strtok(NULL," \t");
}
delete[] strbuf;
}
else
{
} else {
KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
}
@ -204,17 +194,13 @@ void KimInteractions::do_setup(int narg, char **arg)
int sim_model_idx=-1;
for (int i=0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel,i,&sim_lines,&sim_field);
simulatorModel,i,&sim_lines,&sim_field);
if (0 == strcmp(sim_field,"model-defn")) {
sim_model_idx = i;
for (int j=0; j < sim_lines; ++j) {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel,sim_model_idx,j,&sim_value);
char strbuf[MAXLINE];
char * strword;
strcpy(strbuf,sim_value);
strword = strtok(strbuf," \t");
if (0==strcmp(strword,"KIM_SET_TYPE_PARAMETERS")) {
simulatorModel,sim_model_idx,j,&sim_value);
if (utils::strmatch(sim_value,"^KIM_SET_TYPE_PARAMETERS")) {
// Notes regarding the KIM_SET_TYPE_PARAMETERS command
// * This is an INTERNAL command.
// * It is intended for use only by KIM Simulator Models.
@ -226,11 +212,11 @@ void KimInteractions::do_setup(int narg, char **arg)
// * The command is not documented fully as it is expected to be
// temporary. Eventually it should be replaced by a more
// comprehensive symbolic types support in lammps.
KIM_SET_TYPE_PARAMETERS(sim_value);
} else {
KIM_SET_TYPE_PARAMETERS(sim_value);
} else {
input->one(sim_value);
}
}
}
}
}
@ -284,7 +270,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(char const *const input_line) cons
error->one(FLERR,"Parameter file not found");
}
char *species1, *species2, *the_rest, *check;
char *species1, *species2, *the_rest;
std::vector<char *> species;
for (int i = 0; i < atom->ntypes; ++i)
{

4
src/KIM/kim_param.h
View File

@ -81,10 +81,6 @@ public:
private:
void echo_var_assign(const std::string &name, const std::string &value) const;
private:
bool kim_param_get;
bool kim_param_set;
};
} // namespace LAMMPS_NS

16
src/KIM/pair_kim.cpp
View File

@ -285,13 +285,6 @@ void PairKIM::allocate()
void PairKIM::settings(int narg, char **arg)
{
// some of the code below needs to know the number of atom types,
// but that is not set until the simulation box is created.
if (domain->box_exist == 0)
error->all(FLERR,"May not use 'pair_style kim' command before "
"simulation box is defined");
// This is called when "pair_style kim ..." is read from input
// may be called multiple times
++settings_call_count;
@ -312,15 +305,6 @@ void PairKIM::settings(int narg, char **arg)
// first time called will do nothing...
kim_free();
// make sure things are allocated
if (allocated != 1) allocate();
// clear setflag to ensure coeff() is called after settings()
int n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set lmps_* bool flags
set_lmps_flags();

22
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -123,6 +123,8 @@ void FixQEqReaxKokkos<DeviceType>::init()
init_shielding_k();
init_hist();
last_allocate = -1;
}
/* ---------------------------------------------------------------------- */
@ -195,7 +197,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
nlocal = atomKK->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
k_params.template sync<DeviceType>();
@ -207,6 +208,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
inum = list->inum;
ignum = inum + list->gnum;
copymode = 1;
@ -216,8 +218,10 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
// get max number of neighbor
if (!allocated_flag || update->ntimestep == neighbor->lastcall)
if (!allocated_flag || last_allocate < neighbor->lastcall) {
allocate_matrix();
last_allocate = update->ntimestep;
}
// compute_H
@ -289,6 +293,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
// calculate_Q();
k_s_hist.template sync<DeviceType>();
k_t_hist.template sync<DeviceType>();
calculate_q();
k_s_hist.template modify<DeviceType>();
k_t_hist.template modify<DeviceType>();
@ -373,7 +379,6 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array()
}
// init_storage
const int ignum = atom->nlocal + atom->nghost;
FixQEqReaxKokkosZeroFunctor<DeviceType> zero_functor(this);
Kokkos::parallel_for(ignum,zero_functor);
@ -732,7 +737,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
FixQEqReaxKokkosSparse12Functor<DeviceType> sparse12_functor(this);
Kokkos::parallel_for(inum,sparse12_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (neighflag == HALF) {
FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
@ -788,7 +793,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {
@ -869,7 +874,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
FixQEqReaxKokkosSparse32Functor<DeviceType> sparse32_functor(this);
Kokkos::parallel_for(inum,sparse32_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {
@ -927,7 +932,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {
@ -1503,6 +1508,9 @@ int FixQEqReaxKokkos<DeviceType>::pack_exchange(int i, double *buf)
template<class DeviceType>
int FixQEqReaxKokkos<DeviceType>::unpack_exchange(int nlocal, double *buf)
{
k_s_hist.template sync<LMPHostType>();
k_t_hist.template sync<LMPHostType>();
for (int m = 0; m < nprev; m++) s_hist[nlocal][m] = buf[m];
for (int m = 0; m < nprev; m++) t_hist[nlocal][m] = buf[nprev+m];

4
src/KOKKOS/fix_qeq_reax_kokkos.h
View File

@ -151,8 +151,8 @@ class FixQEqReaxKokkos : public FixQEqReax {
double memory_usage();
private:
int inum;
int allocated_flag;
int inum,ignum;
int allocated_flag, last_allocate;
int need_dup;
typename AT::t_int_scalar d_mfill_offset;

42
src/KOKKOS/pair_reaxc_kokkos.cpp
View File

@ -199,6 +199,8 @@ void PairReaxCKokkos<DeviceType>::setup()
hbond_parameters *hbp;
for (i = 1; i <= n; i++) {
if (map[i] == -1) continue;
// general
k_params_sing.h_view(i).mass = system->reax_param.sbp[map[i]].mass;
@ -229,6 +231,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_sing.h_view(i).p_hbond = system->reax_param.sbp[map[i]].p_hbond;
for (j = 1; j <= n; j++) {
if (map[j] == -1) continue;
twbp = &(system->reax_param.tbp[map[i]][map[j]]);
// vdW
@ -270,6 +274,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_twbp.h_view(i,j).p_ovun1 = twbp->p_ovun1;
for (k = 1; k <= n; k++) {
if (map[k] == -1) continue;
// Angular
thbh = &(system->reax_param.thbp[map[i]][map[j]][map[k]]);
thbp = &(thbh->prm[0]);
@ -290,6 +296,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_hbp.h_view(i,j,k).r0_hb = hbp->r0_hb;
for (m = 1; m <= n; m++) {
if (map[m] == -1) continue;
// Torsion
fbh = &(system->reax_param.fbp[map[i]][map[j]][map[k]][map[m]]);
fbp = &(fbh->prm[0]);
@ -377,7 +385,9 @@ void PairReaxCKokkos<DeviceType>::init_md()
d_LR = k_LR.template view<DeviceType>();
for (int i = 1; i <= ntypes; ++i) {
if (map[i] == -1) continue;
for (int j = i; j <= ntypes; ++j) {
if (map[j] == -1) continue;
int n = LR[i][j].n;
if (n == 0) continue;
k_LR.h_view(i,j).dx = LR[i][j].dx;
@ -539,7 +549,9 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
ntypes = atom->ntypes;
for( i = 0; i <= ntypes; ++i ) {
for( j = i; j <= ntypes; ++j )
if (map[i] == -1) continue;
for( j = i; j <= ntypes; ++j ) {
if (map[i] == -1) continue;
if (LR[i][j].n) {
sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" );
sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" );
@ -548,6 +560,7 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" );
sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" );
}
}
sfree( control->error_ptr, LR[i], "LR[i]" );
}
sfree( control->error_ptr, LR, "LR" );
@ -3659,33 +3672,6 @@ void PairReaxCKokkos<DeviceType>::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i,
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void *PairReaxCKokkos<DeviceType>::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str,"chi") == 0 && chi) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) chi[i] = system->reax_param.sbp[map[i]].chi;
else chi[i] = 0.0;
return (void *) chi;
}
if (strcmp(str,"eta") == 0 && eta) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) eta[i] = system->reax_param.sbp[map[i]].eta;
else eta[i] = 0.0;
return (void *) eta;
}
if (strcmp(str,"gamma") == 0 && gamma) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) gamma[i] = system->reax_param.sbp[map[i]].gamma;
else gamma[i] = 0.0;
return (void *) gamma;
}
return NULL;
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)

1
src/KOKKOS/pair_reaxc_kokkos.h
View File

@ -121,7 +121,6 @@ class PairReaxCKokkos : public PairReaxC {
void ev_setup(int, int, int alloc = 1);
void compute(int, int);
void *extract(const char *, int &);
void init_style();
double memory_usage();
void FindBond(int &);

2
src/MISC/fix_ttm.cpp
View File

@ -515,7 +515,7 @@ void FixTTM::end_of_step()
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
fprintf(fp,BIGINT_FORMAT,update->ntimestep);
fmt::print(fp,"{}",update->ntimestep);
double T_a;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)

78
src/RIGID/fix_rigid.cpp
View File

@ -36,6 +36,7 @@
#include "error.h"
#include "rigid_const.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -414,9 +415,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0 &&
strcmp(style,"rigid/nvt/omp") != 0 &&
strcmp(style,"rigid/npt/omp") != 0)
if (!utils::strmatch(style,"^rigid/n.t"))
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
@ -426,9 +425,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
@ -444,9 +441,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
@ -461,9 +456,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
@ -473,9 +466,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
@ -485,9 +476,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
@ -524,9 +513,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0 &&
strcmp(style,"rigid/nvt/omp") != 0 &&
strcmp(style,"rigid/npt/omp") != 0)
if (!utils::strmatch(style,"^rigid/n.t"))
error->all(FLERR,"Illegal fix rigid command");
t_chain = force->inumeric(FLERR,arg[iarg+1]);
t_iter = force->inumeric(FLERR,arg[iarg+2]);
@ -535,9 +522,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
if (!utils::strmatch(style,"^rigid/np."))
error->all(FLERR,"Illegal fix rigid command");
p_chain = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
@ -623,10 +608,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
if (me == 0) {
if (screen) fprintf(screen,"%d rigid bodies with %d atoms\n",nbody,nsum);
if (logfile) fprintf(logfile,"%d rigid bodies with %d atoms\n",nbody,nsum);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} rigid bodies with {} atoms\n",
nbody,nsum));
}
/* ---------------------------------------------------------------------- */
@ -720,12 +704,9 @@ void FixRigid::init()
for (i = 0; i < modify->nfix; i++) {
if (modify->fix[i]->rigid_flag) rflag = 1;
if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix rigid",
modify->fix[i]->id);
error->warning(FLERR,str);
}
!modify->fix[i]->rigid_flag)
error->warning(FLERR,fmt::format("Fix {} alters forces after fix "
"rigid",modify->fix[i]->id));
}
}
@ -2300,12 +2281,9 @@ void FixRigid::readfile(int which, double *vec,
if (me == 0) {
fp = fopen(inpfile,"r");
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open fix rigid inpfile %s",inpfile);
error->one(FLERR,str);
}
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open fix rigid file {}: {}",
inpfile,utils::getsyserror()));
while (1) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of fix rigid file");
@ -2410,19 +2388,15 @@ void FixRigid::write_restart_file(const char *file)
{
if (me) return;
char outfile[128];
snprintf(outfile,128,"%s.rigid",file);
FILE *fp = fopen(outfile,"w");
if (fp == NULL) {
char str[192];
snprintf(str,192,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
auto outfile = std::string(file) + ".rigid";
FILE *fp = fopen(outfile.c_str(),"w");
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open fix rigid restart file {}: {}",
outfile,utils::getsyserror()));
fprintf(fp,"# fix rigid mass, COM, inertia tensor info for "
"%d bodies on timestep " BIGINT_FORMAT "\n\n",
nbody,update->ntimestep);
fprintf(fp,"%d\n",nbody);
fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for "
"{} bodies on timestep {}\n\n",nbody,update->ntimestep);
fmt::print(fp,"{}\n",nbody);
// compute I tensor against xyz axes from diagonalized I and current quat
// Ispace = P Idiag P_transpose

111
src/RIGID/fix_rigid_small.cpp
View File

@ -40,6 +40,7 @@
#include "error.h"
#include "rigid_const.h"
#include "utils.h"
#include "fmt/format.h"
#include <map>
@ -248,8 +249,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
if (!utils::strmatch(style,"^rigid/n.t/small"))
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
@ -259,9 +259,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
@ -276,9 +275,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
@ -292,6 +290,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = force->numeric(FLERR,arg[iarg+3]);
@ -300,6 +300,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
p_period[1] = force->numeric(FLERR,arg[iarg+3]);
@ -308,6 +310,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[2] = force->numeric(FLERR,arg[iarg+3]);
@ -343,20 +347,18 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
if (!utils::strmatch(style,"^rigid/n.t/small"))
error->all(FLERR,"Illegal fix rigid/small command");
t_chain = force->numeric(FLERR,arg[iarg+1]);
t_iter = force->numeric(FLERR,arg[iarg+2]);
t_order = force->numeric(FLERR,arg[iarg+3]);
t_chain = force->inumeric(FLERR,arg[iarg+1]);
t_iter = force->inumeric(FLERR,arg[iarg+2]);
t_order = force->inumeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
if (!utils::strmatch(style,"^rigid/np./small"))
error->all(FLERR,"Illegal fix rigid/small command");
p_chain = force->numeric(FLERR,arg[iarg+1]);
p_chain = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"gravity") == 0) {
@ -406,14 +408,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
create_bodies(bodyID);
if (customflag) delete [] bodyID;
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)
fprintf(screen," create bodies CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," create bodies CPU = %g seconds\n",time2-time1);
}
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" create bodies CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
// set nlocal_body and allocate bodies I own
@ -471,18 +468,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&atomone,&atomall,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen,"%d rigid bodies with " BIGINT_FORMAT " atoms\n",
nbody,atomall);
fprintf(screen," %g = max distance from body owner to body atom\n",
maxextent);
}
if (logfile) {
fprintf(logfile,"%d rigid bodies with " BIGINT_FORMAT " atoms\n",
nbody,atomall);
fprintf(logfile," %g = max distance from body owner to body atom\n",
maxextent);
}
auto msg = fmt::format(" {} rigid bodies with {} atoms\n",nbody,atomall);
msg += fmt::format(" {:.8} = max distance from body owner to body atom\n",
maxextent);
utils::logmesg(lmp,msg);
}
// initialize Marsaglia RNG with processor-unique seed
@ -567,12 +556,9 @@ void FixRigidSmall::init()
for (i = 0; i < modify->nfix; i++) {
if (modify->fix[i]->rigid_flag) rflag = 1;
if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix rigid",
modify->fix[i]->id);
error->warning(FLERR,str);
}
!modify->fix[i]->rigid_flag)
error->warning(FLERR,fmt::format("Fix {} alters forces after fix "
"rigid",modify->fix[i]->id));
}
}
@ -2459,12 +2445,9 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
if (me == 0) {
fp = fopen(inpfile,"r");
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open fix rigid/small inpfile %s",inpfile);
error->one(FLERR,str);
}
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open fix rigid/small file {}: {}",
inpfile,utils::getsyserror()));
while (1) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL)
@ -2574,19 +2557,15 @@ void FixRigidSmall::write_restart_file(const char *file)
// proc 0 opens file and writes header
if (me == 0) {
char outfile[128];
snprintf(outfile,128,"%s.rigid",file);
fp = fopen(outfile,"w");
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
auto outfile = std::string(file) + ".rigid";
fp = fopen(outfile.c_str(),"w");
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open fix rigid restart file {}: {}",
outfile,utils::getsyserror()));
fprintf(fp,"# fix rigid mass, COM, inertia tensor info for "
"%d bodies on timestep " BIGINT_FORMAT "\n\n",
nbody,update->ntimestep);
fprintf(fp,"%d\n",nbody);
fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for "
"{} bodies on timestep {}\n\n",nbody,update->ntimestep);
fmt::print(fp,"{}\n",nbody);
}
// communication buffer for all my rigid body info
@ -3324,15 +3303,11 @@ void FixRigidSmall::reset_atom2body()
atom2body[i] = -1;
if (bodytag[i]) {
iowner = atom->map(bodytag[i]);
if (iowner == -1) {
char str[128];
sprintf(str,
"Rigid body atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
atom->tag[i],bodytag[i],comm->me,update->ntimestep);
error->one(FLERR,str);
if (iowner == -1)
error->one(FLERR,fmt::format("Rigid body atoms {} {} missing on "
"proc {} at step {}",atom->tag[i],
bodytag[i],comm->me,update->ntimestep));
}
atom2body[i] = bodyown[iowner];
}
}

116
src/RIGID/fix_shake.cpp
View File

@ -33,6 +33,7 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -225,14 +226,9 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
find_clusters();
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)
fprintf(screen," find clusters CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," find clusters CPU = %g seconds\n",time2-time1);
}
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" find clusters CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
// initialize list of SHAKE clusters to constrain
@ -525,44 +521,31 @@ void FixShake::pre_neighbor()
if (shake_flag[i] == 2) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
}
if (atom1 == -1 || atom2 == -1)
error->one(FLERR,fmt::format("Shake atoms {} {} missing on proc "
"{} at step {}",shake_atom[i][0],
shake_atom[i][1],me,update->ntimestep));
if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(FLERR,str);
}
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one(FLERR,fmt::format("Shake atoms {} {} {} missing on proc "
"{} at step {}",shake_atom[i][0],
shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep));
if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
error->one(FLERR,str);
}
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,fmt::format("Shake atoms {} {} {} {} missing on "
"proc {} at step {}",shake_atom[i][0],
shake_atom[i][1],shake_atom[i][2],
shake_atom[i][3],me,update->ntimestep));
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
list[nlist++] = i;
}
@ -697,11 +680,10 @@ void FixShake::find_clusters()
tagint tagprev;
double massone;
if (me == 0 && screen) {
if (!rattle) fprintf(screen,"Finding SHAKE clusters ...\n");
else fprintf(screen,"Finding RATTLE clusters ...\n");
if ((me == 0) && screen) {
if (!rattle) fputs("Finding SHAKE clusters ...\n",screen);
else fputs("Finding RATTLE clusters ...\n",screen);
}
atommols = atom->avec->onemols;
tagint *tag = atom->tag;
@ -1024,18 +1006,11 @@ void FixShake::find_clusters()
MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen," %d = # of size 2 clusters\n",count2/2);
fprintf(screen," %d = # of size 3 clusters\n",count3/3);
fprintf(screen," %d = # of size 4 clusters\n",count4/4);
fprintf(screen," %d = # of frozen angles\n",count1/3);
}
if (logfile) {
fprintf(logfile," %d = # of size 2 clusters\n",count2/2);
fprintf(logfile," %d = # of size 3 clusters\n",count3/3);
fprintf(logfile," %d = # of size 4 clusters\n",count4/4);
fprintf(logfile," %d = # of frozen angles\n",count1/3);
}
auto mesg = fmt::format("{:>8} = # of size 2 clusters\n",count2/2);
mesg += fmt::format("{:>8} = # of size 3 clusters\n",count3/3);
mesg += fmt::format("{:>8} = # of size 4 clusters\n",count4/4);
mesg += fmt::format("{:>8} = # of frozen angles\n",count1/3);
utils::logmesg(lmp,mesg);
}
}
@ -2558,34 +2533,21 @@ void FixShake::stats()
// print stats only for non-zero counts
if (me == 0) {
if (screen) {
fprintf(screen,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 1; i < nb; i++)
if (b_count_all[i])
fprintf(screen," %d %g %g %d\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i],
b_count_all[i]);
for (i = 1; i < na; i++)
if (a_count_all[i])
fprintf(screen," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
auto mesg = fmt::format("SHAKE stats (type/ave/delta/count) on step {}\n",
update->ntimestep);
for (i = 1; i < nb; i++) {
const auto bcnt = b_count_all[i];
if (bcnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
b_ave_all[i]/bcnt,b_max_all[i]-b_min_all[i],bcnt);
}
if (logfile) {
fprintf(logfile,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 0; i < nb; i++)
if (b_count_all[i])
fprintf(logfile," %d %g %g\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
for (i = 0; i < na; i++)
if (a_count_all[i])
fprintf(logfile," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
for (i = 1; i < na; i++) {
const auto acnt = a_count_all[i];
if (acnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
a_ave_all[i]/acnt,a_max_all[i]-a_min_all[i],acnt);
}
utils::logmesg(lmp,mesg);
}
// next timestep for stats

8
src/USER-INTEL/fix_intel.cpp
View File

@ -66,6 +66,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
_pair_intel_count = 0;
_hybrid_nonpair = 0;
_print_pkg_info = 1;
_nthreads = comm->nthreads;
_precision_mode = PREC_MODE_MIXED;
_offload_balance = -1.0;
@ -218,12 +219,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
#endif
if (nomp != 0) {
omp_set_num_threads(nomp);
comm->nthreads = nomp;
} else {
int nthreads;
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(nthreads)
nthreads = omp_get_num_threads();
comm->nthreads = nthreads;
_nthreads = comm->nthreads = nomp;
}
#endif

2
src/USER-INTEL/intel_buffers.cpp
View File

@ -35,6 +35,7 @@ IntelBuffers<flt_t, acc_t>::IntelBuffers(class LAMMPS *lmp_in) :
_ncachetag = 0;
_cutneighsq = 0;
_cutneighghostsq = 0;
_need_tag = 0;
#ifdef _LMP_INTEL_OFFLOAD
_separate_buffers = 0;
_off_f = 0;
@ -44,7 +45,6 @@ IntelBuffers<flt_t, acc_t>::IntelBuffers(class LAMMPS *lmp_in) :
_off_threads = 0;
_off_ccache = 0;
_off_ncache = 0;
_need_tag = 0;
_host_nmax = 0;
#endif
}

3
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -33,6 +33,7 @@
#include "citeme.h"
#include "math_const.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -763,7 +764,7 @@ void FixTTMMod::end_of_step()
MPI_Allreduce(&t_surface_l,&surface_l,
1,MPI_INT,MPI_MIN,world);
if (me == 0) {
fprintf(fp,BIGINT_FORMAT,update->ntimestep);
fmt::print(fp,"{}",update->ntimestep);
double T_a;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)

25
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -463,19 +463,26 @@ void FixQEqReax::min_setup_pre_force(int vflag)
void FixQEqReax::init_storage()
{
int NN;
int *ilist;
if (reaxc)
if (reaxc) {
NN = reaxc->list->inum + reaxc->list->gnum;
else
ilist = reaxc->list->ilist;
} else {
NN = list->inum + list->gnum;
ilist = list->ilist;
}
for (int i = 0; i < NN; i++) {
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
b_prm[i] = 0;
s[i] = t[i] = 0;
for (int ii = 0; ii < NN; ii++) {
int i = ilist[ii];
if (atom->mask[i] & groupbit) {
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
b_prm[i] = 0;
s[i] = t[i] = 0;
}
}
}

4
src/USER-REAXC/pair_reaxc.cpp
View File

@ -468,9 +468,11 @@ void PairReaxC::setup( )
write_reax_atoms();
int num_nbrs = estimate_reax_lists();
if (num_nbrs < 0)
error->all(FLERR,"Too many neighbors for pair style reax/c");
if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
lists+FAR_NBRS))
error->one(FLERR,"Pair reax/c problem in far neighbor list");
error->all(FLERR,"Pair reax/c problem in far neighbor list");
(lists+FAR_NBRS)->error_ptr=error;
write_reax_lists();

14
src/USER-REAXC/reaxc_list.cpp
View File

@ -48,44 +48,44 @@ int Make_List(int n, int num_intrs, int type, reax_list *l )
switch(l->type) {
case TYP_VOID:
if (l->select.v) sfree(l->error_ptr, l->select.v, "list:v");
l->select.v = (void*) smalloc(l->error_ptr, l->num_intrs * sizeof(void*), "list:v");
l->select.v = (void*) smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(void*), "list:v");
break;
case TYP_THREE_BODY:
if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies");
l->select.three_body_list = (three_body_interaction_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(three_body_interaction_data),
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(three_body_interaction_data),
"list:three_bodies");
break;
case TYP_BOND:
if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds");
l->select.bond_list = (bond_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(bond_data), "list:bonds");
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(bond_data), "list:bonds");
break;
case TYP_DBO:
if (l->select.dbo_list) sfree(l->error_ptr, l->select.dbo_list,"list:dbonds");
l->select.dbo_list = (dbond_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(dbond_data), "list:dbonds");
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(dbond_data), "list:dbonds");
break;
case TYP_DDELTA:
if (l->select.dDelta_list) sfree(l->error_ptr, l->select.dDelta_list,"list:dDeltas");
l->select.dDelta_list = (dDelta_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(dDelta_data), "list:dDeltas");
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(dDelta_data), "list:dDeltas");
break;
case TYP_FAR_NEIGHBOR:
if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs");
l->select.far_nbr_list = (far_neighbor_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs");
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(far_neighbor_data), "list:far_nbrs");
break;
case TYP_HBOND:
if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds");
l->select.hbond_list = (hbond_data*)
smalloc(l->error_ptr, l->num_intrs * sizeof(hbond_data), "list:hbonds");
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(hbond_data), "list:hbonds");
break;
default:

19
src/USER-REAXC/reaxc_tool_box.cpp
View File

@ -81,14 +81,17 @@ void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name )
if (n <= 0) {
snprintf(errmsg, 256, "Trying to allocate %ld bytes for array %s. "
"returning NULL.", n, name);
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
return NULL;
}
ptr = malloc( n );
if (ptr == NULL) {
snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n, name);
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
}
return ptr;
@ -104,14 +107,16 @@ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const c
if (n <= 0) {
snprintf(errmsg, 256, "Trying to allocate %ld elements for array %s. "
"returning NULL.\n", n, name );
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
return NULL;
}
if (size <= 0) {
snprintf(errmsg, 256, "Elements size for array %s is %ld. "
"returning NULL", name, size );
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
return NULL;
}
@ -119,7 +124,8 @@ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const c
if (ptr == NULL) {
char errmsg[256];
snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n*size, name);
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
}
return ptr;
@ -132,7 +138,8 @@ void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name )
if (ptr == NULL) {
char errmsg[256];
snprintf(errmsg, 256, "Trying to free the already NULL pointer %s", name );
error_ptr->one(FLERR,errmsg);
if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr);
return;
}

3
src/angle_deprecated.cpp
View File

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

6
src/atom.cpp
View File

@ -653,7 +653,7 @@ AtomVec *Atom::new_avec(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (avec_map->find(estyle) != avec_map->end()) {
AtomVecCreator avec_creator = (*avec_map)[estyle];
AtomVecCreator &avec_creator = (*avec_map)[estyle];
return avec_creator(lmp);
}
}
@ -662,7 +662,7 @@ AtomVec *Atom::new_avec(const std::string &style, int trysuffix, int &sflag)
sflag = 2;
std::string estyle = style + "/" + lmp->suffix2;
if (avec_map->find(estyle) != avec_map->end()) {
AtomVecCreator avec_creator = (*avec_map)[estyle];
AtomVecCreator &avec_creator = (*avec_map)[estyle];
return avec_creator(lmp);
}
}
@ -670,7 +670,7 @@ AtomVec *Atom::new_avec(const std::string &style, int trysuffix, int &sflag)
sflag = 0;
if (avec_map->find(style) != avec_map->end()) {
AtomVecCreator avec_creator = (*avec_map)[style];
AtomVecCreator &avec_creator = (*avec_map)[style];
return avec_creator(lmp);
}

3
src/bond_deprecated.cpp
View File

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

16
src/compute_chunk_atom.cpp
View File

@ -64,6 +64,8 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command");
peratom_flag = 1;
scalar_flag = 1;
extscalar = 0;
size_peratom_cols = 0;
create_attribute = 1;
@ -639,6 +641,20 @@ void ComputeChunkAtom::compute_peratom()
for (int i = 0; i < nlocal; i++) chunk[i] = ichunk[i];
}
/* ----------------------------------------------------------------------
to return the number of chunks, we first need to make certain
that compute_peratom() has been called.
------------------------------------------------------------------------- */
double ComputeChunkAtom::compute_scalar()
{
if (invoked_peratom != update->ntimestep)
compute_peratom();
invoked_scalar = update->ntimestep;
return (scalar = nchunk);
}
/* ----------------------------------------------------------------------
set lock, so that nchunk will not change from startstep to stopstep
called by fix for duration of time it requires lock

1
src/compute_chunk_atom.h
View File

@ -39,6 +39,7 @@ class ComputeChunkAtom : public Compute {
void init();
void setup();
void compute_peratom();
double compute_scalar();
void set_arrays(int);
double memory_usage();

3
src/compute_deprecated.cpp
View File

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

188
src/compute_fragment_atom.cpp
View File

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

5
src/compute_fragment_atom.h
View File

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

24
src/deprecated.cpp
View File

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

1
src/deprecated.h
View File

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

3
src/dihedral_deprecated.cpp
View File

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

16
src/domain.cpp
View File

@ -1764,7 +1764,7 @@ void Domain::add_region(int narg, char **arg)
if (lmp->suffix) {
std::string estyle = std::string(arg[1]) + "/" + lmp->suffix;
if (region_map->find(estyle) != region_map->end()) {
RegionCreator region_creator = (*region_map)[estyle];
RegionCreator &region_creator = (*region_map)[estyle];
regions[nregion] = region_creator(lmp, narg, arg);
regions[nregion]->init();
nregion++;
@ -1775,7 +1775,7 @@ void Domain::add_region(int narg, char **arg)
if (lmp->suffix2) {
std::string estyle = std::string(arg[1]) + "/" + lmp->suffix2;
if (region_map->find(estyle) != region_map->end()) {
RegionCreator region_creator = (*region_map)[estyle];
RegionCreator &region_creator = (*region_map)[estyle];
regions[nregion] = region_creator(lmp, narg, arg);
regions[nregion]->init();
nregion++;
@ -1785,7 +1785,7 @@ void Domain::add_region(int narg, char **arg)
}
if (region_map->find(arg[1]) != region_map->end()) {
RegionCreator region_creator = (*region_map)[arg[1]];
RegionCreator &region_creator = (*region_map)[arg[1]];
regions[nregion] = region_creator(lmp, narg, arg);
} else error->all(FLERR,utils::check_packages_for_style("region",arg[1],lmp));
@ -1939,13 +1939,13 @@ void Domain::print_box(const std::string &prefix)
if (comm->me == 0) {
std::string mesg = prefix;
if (triclinic == 0) {
mesg += fmt::format("orthogonal box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
mesg += fmt::format("orthogonal box = ({:.8} {:.8} {:.8}) to "
"({:.8} {:.8} {:.8})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
} else {
mesg += fmt::format("triclinic box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g}) with tilt "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
mesg += fmt::format("triclinic box = ({:.8} {:.8} {:.8}) to "
"({:.8} {:.8} {:.8}) with tilt "
"({:.8} {:.8} {:.8})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2],xy,xz,yz);
}
utils::logmesg(lmp,mesg);

3
src/dump_deprecated.cpp
View File

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

18
src/finish.cpp
View File

@ -462,8 +462,8 @@ void Finish::end(int flag)
} else fraction = flop3 = flop1 = 0.0;
if (me == 0)
utils::logmesg(lmp,fmt::format("FFT time (% of Kspce) = {} ({})\n"
"FFT Gflps 3d (1d only) = {} {}\n",
utils::logmesg(lmp,fmt::format("FFT time (% of Kspce) = {:.6} ({:.4})\n"
"FFT Gflps 3d (1d only) = {:.8} {:.8}\n",
time3d,fraction,flop3,flop1));
}
@ -472,7 +472,7 @@ void Finish::end(int flag)
tmp = atom->nlocal;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
mesg += fmt::format("Nlocal: {} ave {} max {} min\n",ave,max,min);
mesg += fmt::format("Nlocal: {:11.6} ave {:11.6g} max {:11.6g} min\n",ave,max,min);
mesg += "Histogram:";
for (i = 0; i < 10; i++) mesg += fmt::format(" {}",histo[i]);
mesg += "\n";
@ -481,7 +481,7 @@ void Finish::end(int flag)
tmp = atom->nghost;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
mesg += fmt::format("Nghost: {} ave {} max {} min\n",ave,max,min);
mesg += fmt::format("Nghost: {:11.6} ave {:11.6g} max {:11.6g} min\n",ave,max,min);
mesg += "Histogram:";
for (i = 0; i < 10; i++) mesg += fmt::format(" {}",histo[i]);
mesg += "\n";
@ -510,7 +510,7 @@ void Finish::end(int flag)
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
mesg += fmt::format("Neighs: {} ave {} max {} min\n",ave,max,min);
mesg += fmt::format("Neighs: {:11.6} ave {:11.6g} max {:11.6g} min\n",ave,max,min);
mesg += "Histogram:";
for (i = 0; i < 10; i++) mesg += fmt::format(" {}",histo[i]);
mesg += "\n";
@ -538,7 +538,7 @@ void Finish::end(int flag)
tmp = nneighfull;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
mesg += fmt::format("FullNghs: {} ave {} max {} min\n",ave,max,min);
mesg += fmt::format("FullNghs: {:11.6} ave {:11.6g} max {:11.6g} min\n",ave,max,min);
mesg += "Histogram:";
for (i = 0; i < 10; i++) mesg += fmt::format(" {}",histo[i]);
mesg += "\n";
@ -584,11 +584,11 @@ void Finish::end(int flag)
if (me == 0) {
std::string mesg;
mesg += fmt::format("Total # of neighbors = {}\n",static_cast<bigint>(nall));
mesg += fmt::format("Total # of neighbors = {:.8g}\n",nall);
if (atom->natoms > 0)
mesg += fmt::format("Ave neighs/atom = {}\n",nall/atom->natoms);
mesg += fmt::format("Ave neighs/atom = {:.8}\n",nall/atom->natoms);
if (atom->molecular && atom->natoms > 0)
mesg += fmt::format("Ave special neighs/atom = {}\n",
mesg += fmt::format("Ave special neighs/atom = {:.8}\n",
nspec_all/atom->natoms);
mesg += fmt::format("Neighbor list builds = {}\n",neighbor->ncalls);
if (neighbor->dist_check)

3
src/fix_deprecated.cpp
View File

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

36
src/force.cpp
View File

@ -259,7 +259,7 @@ Pair *Force::new_pair(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
PairCreator &pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
@ -267,7 +267,7 @@ Pair *Force::new_pair(const std::string &style, int trysuffix, int &sflag)
sflag = 2;
std::string estyle = style + "/" + lmp->suffix2;
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
PairCreator &pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
@ -276,7 +276,7 @@ Pair *Force::new_pair(const std::string &style, int trysuffix, int &sflag)
sflag = 0;
if (style == "none") return NULL;
if (pair_map->find(style) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[style];
PairCreator &pair_creator = (*pair_map)[style];
return pair_creator(lmp);
}
@ -369,7 +369,7 @@ Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (bond_map->find(estyle) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[estyle];
BondCreator &bond_creator = (*bond_map)[estyle];
return bond_creator(lmp);
}
}
@ -378,7 +378,7 @@ Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag)
sflag = 2;
std::string estyle = style + "/" + lmp->suffix2;
if (bond_map->find(estyle) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[estyle];
BondCreator &bond_creator = (*bond_map)[estyle];
return bond_creator(lmp);
}
}
@ -387,7 +387,7 @@ Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag)
sflag = 0;
if (style == "none") return NULL;
if (bond_map->find(style) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[style];
BondCreator &bond_creator = (*bond_map)[style];
return bond_creator(lmp);
}
@ -446,7 +446,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (angle_map->find(estyle) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[estyle];
AngleCreator &angle_creator = (*angle_map)[estyle];
return angle_creator(lmp);
}
}
@ -455,7 +455,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
sflag = 2;
std::string estyle = style + "/" + lmp->suffix;
if (angle_map->find(estyle) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[estyle];
AngleCreator &angle_creator = (*angle_map)[estyle];
return angle_creator(lmp);
}
}
@ -464,7 +464,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
sflag = 0;
if (style == "none") return NULL;
if (angle_map->find(style) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[style];
AngleCreator &angle_creator = (*angle_map)[style];
return angle_creator(lmp);
}
@ -523,7 +523,7 @@ Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sfla
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (dihedral_map->find(estyle) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
DihedralCreator &dihedral_creator = (*dihedral_map)[estyle];
return dihedral_creator(lmp);
}
}
@ -532,7 +532,7 @@ Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sfla
sflag = 2;
std::string estyle = style + "/" + lmp->suffix2;
if (dihedral_map->find(estyle) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
DihedralCreator &dihedral_creator = (*dihedral_map)[estyle];
return dihedral_creator(lmp);
}
}
@ -541,7 +541,7 @@ Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sfla
sflag = 0;
if (style == "none") return NULL;
if (dihedral_map->find(style) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[style];
DihedralCreator &dihedral_creator = (*dihedral_map)[style];
return dihedral_creator(lmp);
}
@ -600,7 +600,7 @@ Improper *Force::new_improper(const std::string &style, int trysuffix, int &sfla
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (improper_map->find(estyle) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[estyle];
ImproperCreator &improper_creator = (*improper_map)[estyle];
return improper_creator(lmp);
}
}
@ -609,7 +609,7 @@ Improper *Force::new_improper(const std::string &style, int trysuffix, int &sfla
sflag = 2;
std::string estyle = style + "/" + lmp->suffix2;
if (improper_map->find(estyle) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[estyle];
ImproperCreator &improper_creator = (*improper_map)[estyle];
return improper_creator(lmp);
}
}
@ -618,7 +618,7 @@ Improper *Force::new_improper(const std::string &style, int trysuffix, int &sfla
sflag = 0;
if (style == "none") return NULL;
if (improper_map->find(style) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[style];
ImproperCreator &improper_creator = (*improper_map)[style];
return improper_creator(lmp);
}
@ -681,7 +681,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix;
if (kspace_map->find(estyle) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[estyle];
KSpaceCreator &kspace_creator = (*kspace_map)[estyle];
return kspace_creator(lmp);
}
}
@ -690,7 +690,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
sflag = 1;
std::string estyle = style + "/" + lmp->suffix2;
if (kspace_map->find(estyle) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[estyle];
KSpaceCreator &kspace_creator = (*kspace_map)[estyle];
return kspace_creator(lmp);
}
}
@ -699,7 +699,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
sflag = 0;
if (style == "none") return NULL;
if (kspace_map->find(style) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[style];
KSpaceCreator &kspace_creator = (*kspace_map)[style];
return kspace_creator(lmp);
}

3
src/improper_deprecated.cpp
View File

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

32
src/input.cpp
View File

@ -853,7 +853,7 @@ int Input::execute_command()
// invoke commands added via style_command.h
if (command_map->find(command) != command_map->end()) {
CommandCreator command_creator = (*command_map)[command];
CommandCreator &command_creator = (*command_map)[command];
command_creator(lmp,narg,arg);
return 0;
}
@ -1728,13 +1728,9 @@ void Input::package()
if (!modify->check_package("GPU"))
error->all(FLERR,"Package gpu command without GPU package installed");
char **fixarg = new char*[2+narg];
fixarg[0] = (char *) "package_gpu";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "GPU";
for (int i = 1; i < narg; i++) fixarg[i+2] = arg[i];
modify->add_fix(2+narg,fixarg);
delete [] fixarg;
std::string fixcmd = "package_gpu all GPU";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} else if (strcmp(arg[0],"kokkos") == 0) {
if (lmp->kokkos == NULL || lmp->kokkos->kokkos_exists == 0)
@ -1747,26 +1743,18 @@ void Input::package()
error->all(FLERR,
"Package omp command without USER-OMP package installed");
char **fixarg = new char*[2+narg];
fixarg[0] = (char *) "package_omp";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "OMP";
for (int i = 1; i < narg; i++) fixarg[i+2] = arg[i];
modify->add_fix(2+narg,fixarg);
delete [] fixarg;
std::string fixcmd = "package_omp all OMP";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} else if (strcmp(arg[0],"intel") == 0) {
if (!modify->check_package("INTEL"))
error->all(FLERR,
"Package intel command without USER-INTEL package installed");
char **fixarg = new char*[2+narg];
fixarg[0] = (char *) "package_intel";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "INTEL";
for (int i = 1; i < narg; i++) fixarg[i+2] = arg[i];
modify->add_fix(2+narg,fixarg);
delete [] fixarg;
std::string fixcmd = "package_intel all INTEL";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} else error->all(FLERR,"Illegal package command");
}

3
src/kspace_deprecated.cpp
View File

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

2
src/lattice.cpp
View File

@ -305,7 +305,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = "
"{:.8g} {:.8g} {:.8g}\n",
"{:.8} {:.8} {:.8}\n",
xlattice,ylattice,zlattice));
}

10
src/memory.cpp
View File

@ -22,9 +22,13 @@
#include "tbb/scalable_allocator.h"
#else
#include <cstring>
#if defined(__APPLE__)
#include <malloc/malloc.h>
#else
#include <malloc.h>
#endif
#endif
#endif
#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32)
#define LAMMPS_MEMALIGN 64
@ -84,7 +88,13 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name)
if (offset) {
void *optr = ptr;
ptr = smalloc(nbytes, name);
#if defined(__APPLE__)
memcpy(ptr, optr, MIN(nbytes,malloc_size(optr)));
#elif defined(_WIN32) || defined(__MINGW32__)
memcpy(ptr, optr, MIN(nbytes,_msize(optr)));
#else
memcpy(ptr, optr, MIN(nbytes,malloc_usable_size(optr)));
#endif
free(optr);
}
#else

12
src/modify.cpp
View File

@ -872,7 +872,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (lmp->suffix) {
std::string estyle = arg[2] + std::string("/") + lmp->suffix;
if (fix_map->find(estyle) != fix_map->end()) {
FixCreator fix_creator = (*fix_map)[estyle];
FixCreator &fix_creator = (*fix_map)[estyle];
fix[ifix] = fix_creator(lmp,narg,arg);
delete[] fix[ifix]->style;
fix[ifix]->style = new char[estyle.size()+1];
@ -882,7 +882,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (fix[ifix] == NULL && lmp->suffix2) {
std::string estyle = arg[2] + std::string("/") + lmp->suffix2;
if (fix_map->find(estyle) != fix_map->end()) {
FixCreator fix_creator = (*fix_map)[estyle];
FixCreator &fix_creator = (*fix_map)[estyle];
fix[ifix] = fix_creator(lmp,narg,arg);
delete[] fix[ifix]->style;
fix[ifix]->style = new char[estyle.size()+1];
@ -892,7 +892,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
}
if (fix[ifix] == NULL && fix_map->find(arg[2]) != fix_map->end()) {
FixCreator fix_creator = (*fix_map)[arg[2]];
FixCreator &fix_creator = (*fix_map)[arg[2]];
fix[ifix] = fix_creator(lmp,narg,arg);
}
@ -1212,7 +1212,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
if (lmp->suffix) {
std::string estyle = arg[2] + std::string("/") + lmp->suffix;
if (compute_map->find(estyle) != compute_map->end()) {
ComputeCreator compute_creator = (*compute_map)[estyle];
ComputeCreator &compute_creator = (*compute_map)[estyle];
compute[ncompute] = compute_creator(lmp,narg,arg);
delete[] compute[ncompute]->style;
compute[ncompute]->style = new char[estyle.size()+1];
@ -1222,7 +1222,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
if (compute[ncompute] == NULL && lmp->suffix2) {
std::string estyle = arg[2] + std::string("/") + lmp->suffix2;
if (compute_map->find(estyle) != compute_map->end()) {
ComputeCreator compute_creator = (*compute_map)[estyle];
ComputeCreator &compute_creator = (*compute_map)[estyle];
compute[ncompute] = compute_creator(lmp,narg,arg);
delete[] compute[ncompute]->style;
compute[ncompute]->style = new char[estyle.size()+1];
@ -1233,7 +1233,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
if (compute[ncompute] == NULL &&
compute_map->find(arg[2]) != compute_map->end()) {
ComputeCreator compute_creator = (*compute_map)[arg[2]];
ComputeCreator &compute_creator = (*compute_map)[arg[2]];
compute[ncompute] = compute_creator(lmp,narg,arg);
}

6
src/neighbor.cpp
View File

@ -782,7 +782,7 @@ int Neighbor::init_pair()
continue;
}
BinCreator bin_creator = binclass[flag-1];
BinCreator &bin_creator = binclass[flag-1];
neigh_bin[nbin] = bin_creator(lmp);
neigh_bin[nbin]->post_constructor(requests[i]);
neigh_bin[nbin]->istyle = flag;
@ -803,7 +803,7 @@ int Neighbor::init_pair()
continue;
}
StencilCreator stencil_creator = stencilclass[flag-1];
StencilCreator &stencil_creator = stencilclass[flag-1];
neigh_stencil[nstencil] = stencil_creator(lmp);
neigh_stencil[nstencil]->post_constructor(requests[i]);
neigh_stencil[nstencil]->istyle = flag;
@ -828,7 +828,7 @@ int Neighbor::init_pair()
continue;
}
PairCreator pair_creator = pairclass[flag-1];
PairCreator &pair_creator = pairclass[flag-1];
lists[i]->np = neigh_pair[i] = pair_creator(lmp);
neigh_pair[i]->post_constructor(requests[i]);
neigh_pair[i]->istyle = flag;

2
src/output.cpp
View File

@ -568,7 +568,7 @@ void Output::add_dump(int narg, char **arg)
// create the Dump
if (dump_map->find(arg[2]) != dump_map->end()) {
DumpCreator dump_creator = (*dump_map)[arg[2]];
DumpCreator &dump_creator = (*dump_map)[arg[2]];
dump[ndump] = dump_creator(lmp, narg, arg);
} else error->all(FLERR,utils::check_packages_for_style("dump",arg[2],lmp));

3
src/pair_deprecated.cpp
View File

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

2
src/region_deprecated.cpp
View File

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

4
src/replicate.cpp
View File

@ -345,10 +345,10 @@ void Replicate::command(int narg, char **arg)
MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world);
if (me == 0 && screen) {
fprintf(screen," bounding box image = (%i %i %i) to (%i %i %i)\n",
fmt::print(screen," bounding box image = ({} {} {}) to ({} {} {})\n",
_imagelo[0],_imagelo[1],_imagelo[2],
_imagehi[0],_imagehi[1],_imagehi[2]);
fprintf(screen," bounding box extra memory = %.2f MB\n",
fmt::print(screen," bounding box extra memory = {:.2f} MB\n",
(double)size_buf_all*sizeof(double)/1024/1024);
}

42
src/reset_ids.cpp → src/reset_atom_ids.cpp
View File

@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "reset_ids.h"
#include "reset_atom_ids.h"
#include <mpi.h>
#include <cstring>
#include "atom.h"
@ -53,11 +53,11 @@ void ResetIDs::command(int narg, char **arg)
if (domain->box_exist == 0)
error->all(FLERR,"Reset_ids command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use reset_ids unless atoms have IDs");
error->all(FLERR,"Cannot use reset_atom_ids unless atoms have IDs");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->stores_ids)
error->all(FLERR,"Cannot use reset_ids when a fix exists that stores atom IDs");
error->all(FLERR,"Cannot use reset_atom_ids when a fix exists that stores atom IDs");
if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n");
@ -68,12 +68,12 @@ void ResetIDs::command(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_ids command");
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) sortflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) sortflag = 0;
else error->all(FLERR,"Illegal reset_ids command");
else error->all(FLERR,"Illegal reset_atom_ids command");
iarg += 2;
} else error->all(FLERR,"Illegal reset_ids command");
} else error->all(FLERR,"Illegal reset_atom_ids command");
}
// create an atom map if one doesn't exist already
@ -110,7 +110,7 @@ void ResetIDs::command(int narg, char **arg)
int nall = nlocal + atom->nghost;
tagint *oldIDs;
memory->create(oldIDs,nlocal,"reset_ids:oldIDs");
memory->create(oldIDs,nlocal,"reset_atom_ids:oldIDs");
for (int i = 0; i < nlocal; i++) {
oldIDs[i] = tag[i];
@ -129,7 +129,7 @@ void ResetIDs::command(int narg, char **arg)
// forward_comm_array acquires new IDs for ghost atoms
double **newIDs;
memory->create(newIDs,nall,1,"reset_ids:newIDs");
memory->create(newIDs,nall,1,"reset_atom_ids:newIDs");
for (int i = 0; i < nlocal; i++) {
newIDs[i][0] = ubuf(tag[i]).d;
@ -155,7 +155,7 @@ void ResetIDs::command(int narg, char **arg)
for (j = 0; j < num_bond[i]; j++) {
oldID = bond_atom[i][j];
m = atom->map(oldID);
if (m >= 0) bond_atom[i][j] = static_cast<tagint> (newIDs[m][0]);
if (m >= 0) bond_atom[i][j] = (tagint) ubuf(newIDs[m][0]).i;
else badcount++;
}
}
@ -318,6 +318,15 @@ void ResetIDs::sort()
if (dim == 2) mylo[2] = myhi[2] = 0.0;
// must ensure that bounding box volume is > 0.0
for (int i = 0; i < 3; ++i) {
if (mylo[i] == myhi[i]) {
mylo[i] -= 0.5;
myhi[i] += 0.5;
}
}
MPI_Allreduce(mylo,bboxlo,3,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(myhi,bboxhi,3,MPI_DOUBLE,MPI_MAX,world);
@ -332,7 +341,8 @@ void ResetIDs::sort()
// binsize = edge length of a cubic bin
// nbin xyz = bin count in each dimension
bigint nbin_estimate = atom->natoms / PERBIN;
bigint nbin_estimate = atom->natoms / PERBIN + 1;
double vol;
if (dim == 2) vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]);
else vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]) * (bboxhi[2]-bboxlo[2]);
@ -406,8 +416,8 @@ void ResetIDs::sort()
char *buf;
int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous),
0,proclist,
sort_bins,0,buf,sizeof(IDRvous),(void *) this);
0,proclist,
sort_bins,0,buf,sizeof(IDRvous),(void *) this);
IDRvous *outbuf = (IDRvous *) buf;
memory->destroy(proclist);
@ -432,8 +442,8 @@ void ResetIDs::sort()
------------------------------------------------------------------------- */
int ResetIDs::sort_bins(int n, char *inbuf,
int &flag, int *&proclist, char *&outbuf,
void *ptr)
int &flag, int *&proclist, char *&outbuf,
void *ptr)
{
int i,ibin,index;
@ -467,8 +477,8 @@ int ResetIDs::sort_bins(int n, char *inbuf,
for (i = 0; i < n; i++) {
if (in[i].ibin < binlo || in[i].ibin >= binhi) {
//printf("BAD me %d i %d %d ibin %d binlohi %d %d\n",
// rptr->comm->me,i,n,in[i].ibin,binlo,binhi);
error->one(FLERR,"Bad spatial bin assignment in reset_ids sort");
// rptr->comm->me,i,n,in[i].ibin,binlo,binhi);
error->one(FLERR,"Bad spatial bin assignment in reset_atom_ids sort");
}
ibin = in[i].ibin - binlo;
if (head[ibin] < 0) head[ibin] = i;

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

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

214
src/reset_mol_ids.cpp Normal file
View File

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

60
src/reset_mol_ids.h Normal file
View File

@ -0,0 +1,60 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(reset_mol_ids,ResetMolIDs)
#else
#ifndef LMP_RESET_MOL_IDS_H
#define LMP_RESET_MOL_IDS_H
#include "pointers.h"
namespace LAMMPS_NS {
class ResetMolIDs : protected Pointers {
public:
ResetMolIDs(class LAMMPS *);
void command(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Reset_mol_ids command before simulation box is defined
UNDOCUMENTED
E: Can only use reset_mol_ids on molecular systems
UNDOCUMENTED
E: Illegal ... command
UNDOCUMENTED
E: Cannot use reset_mol_ids unless molecules have IDs
UNDOCUMENTED
E: Reset_mol_ids missing %d bond topology atom IDs - use comm_modify cutoff
UNDOCUMENTED
*/

12
src/special.cpp
View File

@ -63,8 +63,8 @@ void Special::build()
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
fmt::print(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" special bond factors lj: {:<8g} {:<8g} {:<8g}\n"
" special bond factors coul: {:<8g} {:<8g} {:<8g}\n",
" special bond factors lj: {:<8} {:<8} {:<8}\n"
" special bond factors coul: {:<8} {:<8} {:<8}\n",
special_lj[1],special_lj[2],special_lj[3],
special_coul[1],special_coul[2],special_coul[3]);
}
@ -93,7 +93,7 @@ void Special::build()
// print max # of 1-2 neighbors
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max # of 1-2 neighbors\n",maxall));
utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-2 neighbors\n",maxall));
// done if special_bond weights for 1-3, 1-4 are set to 1.0
@ -116,7 +116,7 @@ void Special::build()
// print max # of 1-3 neighbors
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max # of 1-3 neighbors\n",maxall));
utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-3 neighbors\n",maxall));
// done if special_bond weights for 1-4 are set to 1.0
@ -139,7 +139,7 @@ void Special::build()
// print max # of 1-4 neighbors
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max # of 1-4 neighbors\n",maxall));
utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-4 neighbors\n",maxall));
// finish processing the onetwo, onethree, onefour lists
@ -691,7 +691,7 @@ void Special::combine()
force->special_extra = 0;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max # of special "
utils::logmesg(lmp,fmt::format("{:>6} = max # of special "
"neighbors\n",atom->maxspecial));
if (lmp->kokkos) {

12
src/update.cpp
View File

@ -331,7 +331,7 @@ void Update::new_integrate(char *style, int narg, char **arg,
sflag = 1;
std::string estyle = style + std::string("/") + lmp->suffix;
if (integrate_map->find(estyle) != integrate_map->end()) {
IntegrateCreator integrate_creator = (*integrate_map)[estyle];
IntegrateCreator &integrate_creator = (*integrate_map)[estyle];
integrate = integrate_creator(lmp, narg, arg);
return;
}
@ -341,7 +341,7 @@ void Update::new_integrate(char *style, int narg, char **arg,
sflag = 2;
std::string estyle = style + std::string("/") + lmp->suffix2;
if (integrate_map->find(estyle) != integrate_map->end()) {
IntegrateCreator integrate_creator = (*integrate_map)[estyle];
IntegrateCreator &integrate_creator = (*integrate_map)[estyle];
integrate = integrate_creator(lmp, narg, arg);
return;
}
@ -350,7 +350,7 @@ void Update::new_integrate(char *style, int narg, char **arg,
sflag = 0;
if (integrate_map->find(style) != integrate_map->end()) {
IntegrateCreator integrate_creator = (*integrate_map)[style];
IntegrateCreator &integrate_creator = (*integrate_map)[style];
integrate = integrate_creator(lmp, narg, arg);
return;
}
@ -402,7 +402,7 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */,
sflag = 1;
std::string estyle = style + std::string("/") + lmp->suffix;
if (minimize_map->find(estyle) != minimize_map->end()) {
MinimizeCreator minimize_creator = (*minimize_map)[estyle];
MinimizeCreator &minimize_creator = (*minimize_map)[estyle];
minimize = minimize_creator(lmp);
return;
}
@ -412,7 +412,7 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */,
sflag = 2;
std::string estyle = style + std::string("/") + lmp->suffix2;
if (minimize_map->find(estyle) != minimize_map->end()) {
MinimizeCreator minimize_creator = (*minimize_map)[estyle];
MinimizeCreator &minimize_creator = (*minimize_map)[estyle];
minimize = minimize_creator(lmp);
return;
}
@ -421,7 +421,7 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */,
sflag = 0;
if (minimize_map->find(style) != minimize_map->end()) {
MinimizeCreator minimize_creator = (*minimize_map)[style];
MinimizeCreator &minimize_creator = (*minimize_map)[style];
minimize = minimize_creator(lmp);
return;
}

5
unittest/commands/CMakeLists.txt
View File

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

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

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

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

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

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

@ -0,0 +1,562 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom.h"
#include "fmt/format.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "output.h"
#include "update.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
using LAMMPS_NS::utils::split_words;
namespace LAMMPS_NS {
using ::testing::MatchesRegex;
#define GETIDX(i) lmp->atom->map(i)
#define TEST_FAILURE(...) \
if (Info::has_exceptions()) { \
ASSERT_ANY_THROW({__VA_ARGS__}); \
} else { \
ASSERT_DEATH({__VA_ARGS__}, ""); \
}
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
class ResetIDsTest : public ::testing::Test {
protected:
LAMMPS *lmp;
void SetUp() override
{
const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
Info *info = new Info(lmp);
if (info->has_style("atom", "full")) {
lmp->input->one("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER));
lmp->input->one("include ${input_dir}/in.fourmol");
}
delete info;
if (!verbose) ::testing::internal::GetCapturedStdout();
}
void TearDown() override
{
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
}
};
TEST_F(ResetIDsTest, MolIDAll)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 3);
ASSERT_EQ(molid[GETIDX(19)], 3);
ASSERT_EQ(molid[GETIDX(20)], 3);
ASSERT_EQ(molid[GETIDX(21)], 4);
ASSERT_EQ(molid[GETIDX(22)], 4);
ASSERT_EQ(molid[GETIDX(23)], 4);
ASSERT_EQ(molid[GETIDX(24)], 5);
ASSERT_EQ(molid[GETIDX(25)], 5);
ASSERT_EQ(molid[GETIDX(26)], 5);
ASSERT_EQ(molid[GETIDX(27)], 6);
ASSERT_EQ(molid[GETIDX(28)], 6);
ASSERT_EQ(molid[GETIDX(29)], 6);
// the original data file has two different molecule IDs
// for two residues of the same molecule/fragment.
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 4);
ASSERT_EQ(molid[GETIDX(26)], 4);
ASSERT_EQ(molid[GETIDX(27)], 5);
ASSERT_EQ(molid[GETIDX(28)], 5);
ASSERT_EQ(molid[GETIDX(29)], 5);
}
TEST_F(ResetIDsTest, DeletePlusAtomID)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group twowater molecule 4:6:2");
lmp->input->one("delete_atoms group twowater compress no bond yes");
lmp->input->one("reset_mol_ids all");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(24)], 3);
ASSERT_EQ(molid[GETIDX(25)], 3);
ASSERT_EQ(molid[GETIDX(26)], 3);
// now also check and reset the atom ids
ASSERT_GE(GETIDX(1), 0);
ASSERT_GE(GETIDX(2), 0);
ASSERT_GE(GETIDX(3), 0);
ASSERT_GE(GETIDX(4), 0);
ASSERT_GE(GETIDX(5), 0);
ASSERT_GE(GETIDX(6), 0);
ASSERT_GE(GETIDX(7), 0);
ASSERT_GE(GETIDX(8), 0);
ASSERT_GE(GETIDX(9), 0);
ASSERT_GE(GETIDX(10), 0);
ASSERT_GE(GETIDX(11), 0);
ASSERT_GE(GETIDX(12), 0);
ASSERT_GE(GETIDX(13), 0);
ASSERT_GE(GETIDX(14), 0);
ASSERT_GE(GETIDX(15), 0);
ASSERT_GE(GETIDX(16), 0);
ASSERT_GE(GETIDX(17), 0);
ASSERT_GE(GETIDX(18), 0);
ASSERT_GE(GETIDX(19), 0);
ASSERT_GE(GETIDX(20), 0);
ASSERT_EQ(GETIDX(21), -1);
ASSERT_EQ(GETIDX(22), -1);
ASSERT_EQ(GETIDX(23), -1);
ASSERT_GE(GETIDX(24), 0);
ASSERT_GE(GETIDX(25), 0);
ASSERT_GE(GETIDX(26), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_atom_ids");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
for (int i = 1; i <= 23; ++i)
ASSERT_GE(GETIDX(i), 0);
}
TEST_F(ResetIDsTest, PartialOffset)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group nowater subtract all allwater");
lmp->input->one("reset_mol_ids allwater offset 4");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 29);
ASSERT_EQ(lmp->atom->map_tag_max, 29);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 5);
ASSERT_EQ(molid[GETIDX(19)], 5);
ASSERT_EQ(molid[GETIDX(20)], 5);
ASSERT_EQ(molid[GETIDX(21)], 6);
ASSERT_EQ(molid[GETIDX(22)], 6);
ASSERT_EQ(molid[GETIDX(23)], 6);
ASSERT_EQ(molid[GETIDX(24)], 7);
ASSERT_EQ(molid[GETIDX(25)], 7);
ASSERT_EQ(molid[GETIDX(26)], 7);
ASSERT_EQ(molid[GETIDX(27)], 8);
ASSERT_EQ(molid[GETIDX(28)], 8);
ASSERT_EQ(molid[GETIDX(29)], 8);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids nowater offset 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 1);
ASSERT_EQ(molid[GETIDX(9)], 1);
ASSERT_EQ(molid[GETIDX(10)], 1);
ASSERT_EQ(molid[GETIDX(11)], 1);
ASSERT_EQ(molid[GETIDX(12)], 1);
ASSERT_EQ(molid[GETIDX(13)], 1);
ASSERT_EQ(molid[GETIDX(14)], 1);
ASSERT_EQ(molid[GETIDX(15)], 1);
ASSERT_EQ(molid[GETIDX(16)], 1);
ASSERT_EQ(molid[GETIDX(17)], 1);
ASSERT_EQ(molid[GETIDX(18)], 5);
ASSERT_EQ(molid[GETIDX(19)], 5);
ASSERT_EQ(molid[GETIDX(20)], 5);
ASSERT_EQ(molid[GETIDX(21)], 6);
ASSERT_EQ(molid[GETIDX(22)], 6);
ASSERT_EQ(molid[GETIDX(23)], 6);
ASSERT_EQ(molid[GETIDX(24)], 7);
ASSERT_EQ(molid[GETIDX(25)], 7);
ASSERT_EQ(molid[GETIDX(26)], 7);
ASSERT_EQ(molid[GETIDX(27)], 8);
ASSERT_EQ(molid[GETIDX(28)], 8);
ASSERT_EQ(molid[GETIDX(29)], 8);
}
TEST_F(ResetIDsTest, DeleteAdd)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
auto molid = lmp->atom->molecule;
// delete two water molecules
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("group allwater molecule 3:6");
lmp->input->one("group twowater molecule 4:6:2");
lmp->input->one("group nowater subtract all allwater");
lmp->input->one("delete_atoms group twowater compress no bond yes mol yes");
lmp->input->one("reset_mol_ids allwater");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
ASSERT_EQ(molid[GETIDX(1)], 1);
ASSERT_EQ(molid[GETIDX(2)], 1);
ASSERT_EQ(molid[GETIDX(3)], 1);
ASSERT_EQ(molid[GETIDX(4)], 1);
ASSERT_EQ(molid[GETIDX(5)], 1);
ASSERT_EQ(molid[GETIDX(6)], 1);
ASSERT_EQ(molid[GETIDX(7)], 1);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 2);
ASSERT_EQ(molid[GETIDX(14)], 2);
ASSERT_EQ(molid[GETIDX(15)], 2);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 3);
ASSERT_EQ(molid[GETIDX(19)], 3);
ASSERT_EQ(molid[GETIDX(20)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 4);
ASSERT_EQ(molid[GETIDX(26)], 4);
// now also check and reset the atom ids
ASSERT_GE(GETIDX(1), 0);
ASSERT_GE(GETIDX(2), 0);
ASSERT_GE(GETIDX(3), 0);
ASSERT_GE(GETIDX(4), 0);
ASSERT_GE(GETIDX(5), 0);
ASSERT_GE(GETIDX(6), 0);
ASSERT_GE(GETIDX(7), 0);
ASSERT_GE(GETIDX(8), 0);
ASSERT_GE(GETIDX(9), 0);
ASSERT_GE(GETIDX(10), 0);
ASSERT_GE(GETIDX(11), 0);
ASSERT_GE(GETIDX(12), 0);
ASSERT_GE(GETIDX(13), 0);
ASSERT_GE(GETIDX(14), 0);
ASSERT_GE(GETIDX(15), 0);
ASSERT_GE(GETIDX(16), 0);
ASSERT_GE(GETIDX(17), 0);
ASSERT_GE(GETIDX(18), 0);
ASSERT_GE(GETIDX(19), 0);
ASSERT_GE(GETIDX(20), 0);
ASSERT_EQ(GETIDX(21), -1);
ASSERT_EQ(GETIDX(22), -1);
ASSERT_EQ(GETIDX(23), -1);
ASSERT_GE(GETIDX(24), 0);
ASSERT_GE(GETIDX(25), 0);
ASSERT_GE(GETIDX(26), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_atom_ids sort yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
for (int i = 1; i <= 23; ++i)
ASSERT_GE(GETIDX(i), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids nowater offset 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(1)], 2);
ASSERT_EQ(molid[GETIDX(2)], 2);
ASSERT_EQ(molid[GETIDX(3)], 2);
ASSERT_EQ(molid[GETIDX(4)], 2);
ASSERT_EQ(molid[GETIDX(5)], 2);
ASSERT_EQ(molid[GETIDX(6)], 2);
ASSERT_EQ(molid[GETIDX(7)], 2);
ASSERT_EQ(molid[GETIDX(8)], 2);
ASSERT_EQ(molid[GETIDX(9)], 2);
ASSERT_EQ(molid[GETIDX(10)], 2);
ASSERT_EQ(molid[GETIDX(11)], 2);
ASSERT_EQ(molid[GETIDX(12)], 2);
ASSERT_EQ(molid[GETIDX(13)], 3);
ASSERT_EQ(molid[GETIDX(14)], 3);
ASSERT_EQ(molid[GETIDX(15)], 3);
ASSERT_EQ(molid[GETIDX(16)], 2);
ASSERT_EQ(molid[GETIDX(17)], 2);
ASSERT_EQ(molid[GETIDX(18)], 2);
ASSERT_EQ(molid[GETIDX(19)], 2);
ASSERT_EQ(molid[GETIDX(20)], 2);
ASSERT_EQ(molid[GETIDX(21)], 4);
ASSERT_EQ(molid[GETIDX(22)], 4);
ASSERT_EQ(molid[GETIDX(23)], 4);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("create_atoms 1 single 0.0 0.0 0.0");
lmp->input->one("create_atoms 2 single 1.0 0.0 0.0");
lmp->input->one("create_atoms 3 single 2.0 0.0 0.0");
lmp->input->one("create_atoms 4 single 3.0 0.0 0.0");
lmp->input->one("reset_mol_ids all single yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->atom->natoms, 27);
ASSERT_EQ(lmp->atom->map_tag_max, 27);
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 4);
ASSERT_EQ(molid[GETIDX(25)], 5);
ASSERT_EQ(molid[GETIDX(26)], 6);
ASSERT_EQ(molid[GETIDX(27)], 7);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all single no");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(21)], 3);
ASSERT_EQ(molid[GETIDX(22)], 3);
ASSERT_EQ(molid[GETIDX(23)], 3);
ASSERT_EQ(molid[GETIDX(24)], 0);
ASSERT_EQ(molid[GETIDX(25)], 0);
ASSERT_EQ(molid[GETIDX(26)], 0);
ASSERT_EQ(molid[GETIDX(27)], 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_mol_ids all compress no single yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(molid[GETIDX(21)], 21);
ASSERT_EQ(molid[GETIDX(22)], 21);
ASSERT_EQ(molid[GETIDX(23)], 21);
ASSERT_EQ(molid[GETIDX(24)], 24);
ASSERT_EQ(molid[GETIDX(25)], 25);
ASSERT_EQ(molid[GETIDX(26)], 26);
ASSERT_EQ(molid[GETIDX(27)], 27);
}
TEST_F(ResetIDsTest, DeathTests)
{
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids"););
auto mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset 1 1"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset -2"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR on proc 0: Expected integer.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress yes single no offset xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR on proc 0: Expected integer.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all offset"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all compress xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all single"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all single xxx"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*"));
}
TEST(ResetMolIds, CMDFail)
{
LAMMPS *lmp;
const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
if (!verbose) ::testing::internal::GetCapturedStdout();
::testing::internal::CaptureStdout();
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
auto mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Reset_mol_ids command before.*"));
::testing::internal::CaptureStdout();
lmp->input->one("atom_modify id no");
lmp->input->one("region box block 0 1 0 1 0 1");
lmp->input->one("create_box 1 box");
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Cannot use reset_mol_ids unl.*"));
::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("region box block 0 1 0 1 0 1");
lmp->input->one("create_box 1 box");
TEST_FAILURE(lmp->input->one("reset_mol_ids all"););
mesg = ::testing::internal::GetCapturedStdout();
ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Can only use reset_mol_ids.*"));
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
};
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}

26
unittest/force-styles/CMakeLists.txt
View File

@ -30,10 +30,10 @@ target_link_libraries(test_error_stats PRIVATE GTest::GTestMain GTest::GTest)
add_test(NAME ErrorStats COMMAND test_error_stats)
# pair style tester
add_executable(pair_style pair_style.cpp)
target_link_libraries(pair_style PRIVATE lammps style_tests)
add_executable(test_pair_style test_pair_style.cpp)
target_link_libraries(test_pair_style PRIVATE lammps style_tests)
if(FFT_SINGLE)
target_compile_definitions(pair_style PRIVATE -DFFT_SINGLE)
target_compile_definitions(test_pair_style PRIVATE -DFFT_SINGLE)
endif()
# tests for a molecular systems and related pair styles
@ -44,7 +44,7 @@ if (FFT_SINGLE)
endif()
foreach(TEST ${MOL_PAIR_TESTS})
string(REGEX REPLACE "^.*mol-pair-(.*)\.yaml" "MolPairStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()
@ -52,7 +52,7 @@ endforeach()
file(GLOB ATOMIC_PAIR_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/atomic-pair-*.yaml)
foreach(TEST ${ATOMIC_PAIR_TESTS})
string(REGEX REPLACE "^.*atomic-pair-(.*)\.yaml" "AtomicPairStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()
@ -60,29 +60,29 @@ endforeach()
file(GLOB MANYBODY_PAIR_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/manybody-pair-*.yaml)
foreach(TEST ${MANYBODY_PAIR_TESTS})
string(REGEX REPLACE "^.*manybody-pair-(.*)\.yaml" "ManybodyPairStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()
# bond style tester
add_executable(bond_style bond_style.cpp)
target_link_libraries(bond_style PRIVATE lammps style_tests)
add_executable(test_bond_style test_bond_style.cpp)
target_link_libraries(test_bond_style PRIVATE lammps style_tests)
file(GLOB BOND_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/bond-*.yaml)
foreach(TEST ${BOND_TESTS})
string(REGEX REPLACE "^.*bond-(.*)\.yaml" "BondStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND bond_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_bond_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()
# angle style tester
add_executable(angle_style angle_style.cpp)
target_link_libraries(angle_style PRIVATE lammps style_tests)
add_executable(test_angle_style test_angle_style.cpp)
target_link_libraries(test_angle_style PRIVATE lammps style_tests)
file(GLOB ANGLE_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/angle-*.yaml)
foreach(TEST ${ANGLE_TESTS})
string(REGEX REPLACE "^.*angle-(.*)\.yaml" "AngleStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND angle_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_angle_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()
@ -94,6 +94,6 @@ if (FFT_SINGLE)
endif()
foreach(TEST ${KSPACE_TESTS})
string(REGEX REPLACE "^.*kspace-(.*)\.yaml" "KSpaceStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_test(NAME ${TNAME} COMMAND test_pair_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endforeach()

104
unittest/force-styles/angle_style.cpp → unittest/force-styles/test_angle_style.cpp
View File

@ -26,6 +26,7 @@
#include "angle.h"
#include "atom.h"
#include "compute.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
#include "input.h"
@ -40,7 +41,6 @@
#include <ctime>
#include <mpi.h>
#include <iostream>
#include <map>
#include <string>
#include <utility>
@ -230,9 +230,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
return;
}
const int natoms = lmp->atom->natoms;
const int bufsize = 256;
char buf[bufsize];
const int natoms = lmp->atom->natoms;
std::string block("");
YamlWriter writer(outfile);
@ -284,20 +282,16 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
writer.emit_block("angle_coeff", block);
// equilibrium angle
std::stringstream eqstr;
eqstr << lmp->atom->nangletypes;
for (int i = 0; i < lmp->atom->nangletypes; ++i) {
eqstr << " " << lmp->force->angle->equilibrium_angle(i + 1);
}
writer.emit("equilibrium", eqstr.str());
block = fmt::format("{}", lmp->atom->nangletypes);
for (int i = 0; i < lmp->atom->nangletypes; ++i)
block += fmt::format(" {}", lmp->force->angle->equilibrium_angle(i + 1));
writer.emit("equilibrium", block);
// extract
block.clear();
std::stringstream outstr;
for (auto &data : config.extract) {
outstr << data.first << " " << data.second << std::endl;
}
writer.emit_block("extract", outstr.str());
for (auto data : config.extract)
block += fmt::format("{} {}\n", data.first, data.second);
writer.emit_block("extract", block);
// natoms
writer.emit("natoms", natoms);
@ -306,19 +300,18 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
writer.emit("init_energy", lmp->force->angle->energy);
// init_stress
double *stress = lmp->force->angle->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", buf);
auto stress = lmp->force->angle->virial;
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", block);
// init_forces
block.clear();
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("init_forces", block);
@ -330,17 +323,16 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// run_stress
stress = lmp->force->angle->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", buf);
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", block);
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("run_forces", block);
@ -378,8 +370,9 @@ TEST(AngleStyle, plain)
ASSERT_EQ(lmp->atom->natoms, nlocal);
double epsilon = test_config.epsilon;
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
ErrorStats stats;
stats.reset();
const std::vector<coord_t> &f_ref = test_config.init_forces;
@ -391,8 +384,8 @@ TEST(AngleStyle, plain)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Angle *angle = lmp->force->angle;
double *stress = angle->virial;
auto angle = lmp->force->angle;
auto stress = angle->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
@ -410,8 +403,10 @@ TEST(AngleStyle, plain)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = angle->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = angle->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -477,6 +472,7 @@ TEST(AngleStyle, plain)
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = angle->virial;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
@ -601,9 +597,11 @@ TEST(AngleStyle, omp)
ASSERT_EQ(lmp->atom->natoms, nlocal);
// relax error a bit for USER-OMP package
double epsilon = 5.0 * test_config.epsilon;
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
double epsilon = 5.0 * test_config.epsilon;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
@ -614,8 +612,8 @@ TEST(AngleStyle, omp)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Angle *angle = lmp->force->angle;
double *stress = angle->virial;
auto angle = lmp->force->angle;
auto stress = angle->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
@ -634,8 +632,10 @@ TEST(AngleStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = angle->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = angle->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -703,7 +703,8 @@ TEST(AngleStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
@ -797,14 +798,9 @@ TEST(AngleStyle, single)
command("atom_modify map array");
command("region box block -10.0 10.0 -10.0 10.0 -10.0 10.0 units box");
char buf[10];
std::string cmd("create_box 1 box");
cmd += " angle/types ";
snprintf(buf, 10, "%d", nangletypes);
cmd += buf;
cmd += " extra/angle/per/atom 2";
cmd += " extra/special/per/atom 2";
command(cmd);
command(fmt::format("create_box 1 box angle/types {} "
"extra/angle/per/atom 2 extra/special/per/atom 2",
nangletypes));
command("pair_style zero 8.0");
command("pair_coeff * *");

113
unittest/force-styles/bond_style.cpp → unittest/force-styles/test_bond_style.cpp
View File

@ -26,6 +26,7 @@
#include "atom.h"
#include "bond.h"
#include "compute.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
#include "input.h"
@ -40,7 +41,6 @@
#include <ctime>
#include <mpi.h>
#include <iostream>
#include <map>
#include <string>
#include <utility>
@ -230,9 +230,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
return;
}
const int natoms = lmp->atom->natoms;
const int bufsize = 256;
char buf[bufsize];
const int natoms = lmp->atom->natoms;
std::string block("");
YamlWriter writer(outfile);
@ -284,20 +282,16 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
writer.emit_block("bond_coeff", block);
// equilibrium distance
std::stringstream eqstr;
eqstr << lmp->atom->nbondtypes;
for (int i = 0; i < lmp->atom->nbondtypes; ++i) {
eqstr << " " << lmp->force->bond->equilibrium_distance(i + 1);
}
writer.emit("equilibrium", eqstr.str());
block = fmt::format("{}", lmp->atom->nbondtypes);
for (int i = 0; i < lmp->atom->nbondtypes; ++i)
block += fmt::format(" {}", lmp->force->bond->equilibrium_distance(i + 1));
writer.emit("equilibrium", block);
// extract
block.clear();
std::stringstream outstr;
for (auto &data : config.extract) {
outstr << data.first << " " << data.second << std::endl;
}
writer.emit_block("extract", outstr.str());
for (auto data : config.extract)
block += fmt::format("{} {}\n", data.first, data.second);
writer.emit_block("extract", block);
// natoms
writer.emit("natoms", natoms);
@ -306,19 +300,18 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
writer.emit("init_energy", lmp->force->bond->energy);
// init_stress
double *stress = lmp->force->bond->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", buf);
auto stress = lmp->force->bond->virial;
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", block);
// init_forces
block.clear();
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("init_forces", block);
@ -330,17 +323,16 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// run_stress
stress = lmp->force->bond->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", buf);
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", block);
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("run_forces", block);
@ -378,8 +370,9 @@ TEST(BondStyle, plain)
ASSERT_EQ(lmp->atom->natoms, nlocal);
double epsilon = test_config.epsilon;
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
ErrorStats stats;
stats.reset();
const std::vector<coord_t> &f_ref = test_config.init_forces;
@ -391,8 +384,8 @@ TEST(BondStyle, plain)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Bond *bond = lmp->force->bond;
double *stress = bond->virial;
auto bond = lmp->force->bond;
auto stress = bond->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
@ -410,8 +403,10 @@ TEST(BondStyle, plain)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = bond->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = bond->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -477,6 +472,7 @@ TEST(BondStyle, plain)
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = bond->virial;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
@ -601,9 +597,11 @@ TEST(BondStyle, omp)
ASSERT_EQ(lmp->atom->natoms, nlocal);
// relax error a bit for USER-OMP package
double epsilon = 5.0 * test_config.epsilon;
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
double epsilon = 5.0 * test_config.epsilon;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
@ -614,8 +612,8 @@ TEST(BondStyle, omp)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Bond *bond = lmp->force->bond;
double *stress = bond->virial;
auto bond = lmp->force->bond;
auto stress = bond->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon);
@ -633,8 +631,10 @@ TEST(BondStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = bond->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = bond->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -702,7 +702,8 @@ TEST(BondStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
@ -796,20 +797,15 @@ TEST(BondStyle, single)
command("atom_modify map array");
command("region box block -10.0 10.0 -10.0 10.0 -10.0 10.0 units box");
char buf[10];
std::string cmd("create_box 1 box");
cmd += " bond/types ";
snprintf(buf, 10, "%d", nbondtypes);
cmd += buf;
cmd += " extra/bond/per/atom 2";
cmd += " extra/special/per/atom 2";
command(cmd);
command(fmt::format("create_box 1 box bond/types {} "
"extra/bond/per/atom 2 extra/special/per/atom 2",
nbondtypes));
command("pair_style zero 8.0");
command("pair_coeff * *");
command("bond_style " + test_config.bond_style);
Bond *bond = lmp->force->bond;
auto bond = lmp->force->bond;
for (auto &bond_coeff : test_config.bond_coeff) {
command("bond_coeff " + bond_coeff);
@ -1017,9 +1013,10 @@ TEST(BondStyle, extract)
}
GTEST_SKIP();
}
Bond *bond = lmp->force->bond;
void *ptr = nullptr;
int dim = 0;
auto bond = lmp->force->bond;
void *ptr = nullptr;
int dim = 0;
for (auto extract : test_config.extract) {
ptr = bond->extract(extract.first.c_str(), dim);
EXPECT_NE(ptr, nullptr);

127
unittest/force-styles/pair_style.cpp → unittest/force-styles/test_pair_style.cpp
View File

@ -25,6 +25,7 @@
#include "atom.h"
#include "compute.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
#include "input.h"
@ -42,7 +43,6 @@
#include <ctime>
#include <mpi.h>
#include <iostream>
#include <map>
#include <string>
#include <utility>
@ -64,6 +64,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
delete_file(cfg.basename + ".data");
delete_file(cfg.basename + "-coeffs.in");
delete lmp;
lmp = nullptr;
}
LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool newton = true)
@ -231,9 +232,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
return;
}
const int natoms = lmp->atom->natoms;
const int bufsize = 256;
char buf[bufsize];
const int natoms = lmp->atom->natoms;
std::string block("");
YamlWriter writer(outfile);
@ -252,21 +251,21 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// prerequisites
block.clear();
for (auto prerequisite : config.prerequisites) {
for (auto &prerequisite : config.prerequisites) {
block += prerequisite.first + " " + prerequisite.second + "\n";
}
writer.emit_block("prerequisites", block);
// pre_commands
block.clear();
for (auto command : config.pre_commands) {
for (auto &command : config.pre_commands) {
block += command + "\n";
}
writer.emit_block("pre_commands", block);
// post_commands
block.clear();
for (auto command : config.post_commands) {
for (auto &command : config.post_commands) {
block += command + "\n";
}
writer.emit_block("post_commands", block);
@ -286,11 +285,9 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// extract
block.clear();
std::stringstream outstr;
for (auto data : config.extract) {
outstr << data.first << " " << data.second << std::endl;
}
writer.emit_block("extract", outstr.str());
for (auto data : config.extract)
block += fmt::format("{} {}\n", data.first, data.second);
writer.emit_block("extract", block);
// natoms
writer.emit("natoms", natoms);
@ -302,19 +299,18 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
writer.emit("init_coul", lmp->force->pair->eng_coul);
// init_stress
double *stress = lmp->force->pair->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", buf);
auto stress = lmp->force->pair->virial;
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", block);
// init_forces
block.clear();
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("init_forces", block);
@ -329,17 +325,16 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// run_stress
stress = lmp->force->pair->virial;
snprintf(buf, bufsize, "% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", buf);
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", block);
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 0; i < natoms; ++i) {
snprintf(buf, bufsize, "% 3d % 23.16e % 23.16e % 23.16e\n", (int)tag[i], f[i][0], f[i][1],
f[i][2]);
block += buf;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("run_forces", block);
@ -363,7 +358,7 @@ TEST(PairStyle, plain)
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto prerequisite : test_config.prerequisites) {
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
@ -382,8 +377,8 @@ TEST(PairStyle, plain)
if (lmp->force->kspace && lmp->force->kspace->compute_flag)
if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
ErrorStats stats;
stats.reset();
const std::vector<coord_t> &f_ref = test_config.init_forces;
@ -395,8 +390,8 @@ TEST(PairStyle, plain)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Pair *pair = lmp->force->pair;
double *stress = pair->virial;
auto pair = lmp->force->pair;
auto stress = pair->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
@ -415,8 +410,10 @@ TEST(PairStyle, plain)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = pair->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = pair->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -442,7 +439,9 @@ TEST(PairStyle, plain)
double energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon);
EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon);
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon);
// skip comparing per-atom energy with total energy for "kim"
if (std::string("kim") != lmp->force->pair_style)
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
@ -484,6 +483,7 @@ TEST(PairStyle, plain)
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = pair->virial;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
@ -508,7 +508,9 @@ TEST(PairStyle, plain)
energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon);
EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon);
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon);
// skip comparing per-atom energy with total energy for "kim"
if (std::string("kim") != lmp->force->pair_style)
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl;
}
@ -639,7 +641,7 @@ TEST(PairStyle, omp)
if (!lmp) {
std::cerr << "One or more prerequisite styles with /omp suffix\n"
"are not available in this LAMMPS configuration:\n";
for (auto prerequisite : test_config.prerequisites) {
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
@ -659,8 +661,9 @@ TEST(PairStyle, omp)
if (lmp->force->kspace && lmp->force->kspace->compute_flag)
if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
@ -671,8 +674,8 @@ TEST(PairStyle, omp)
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
Pair *pair = lmp->force->pair;
double *stress = pair->virial;
auto pair = lmp->force->pair;
auto stress = pair->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon);
@ -691,8 +694,10 @@ TEST(PairStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = pair->virial;
f = lmp->atom->f;
stress = pair->virial;
tag = lmp->atom->tag;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -759,7 +764,8 @@ TEST(PairStyle, omp)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 5 * epsilon);
@ -824,7 +830,7 @@ TEST(PairStyle, intel)
GTEST_SKIP();
}
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style,"^pppm/disp/intel")) {
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm/disp/intel")) {
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
@ -855,8 +861,9 @@ TEST(PairStyle, intel)
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
@ -887,8 +894,10 @@ TEST(PairStyle, intel)
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
stress = pair->virial;
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = pair->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
@ -963,8 +972,9 @@ TEST(PairStyle, opt)
if (lmp->force->kspace && lmp->force->kspace->compute_flag)
if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
double **f = lmp->atom->f;
tagint *tag = lmp->atom->tag;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
@ -996,6 +1006,7 @@ TEST(PairStyle, opt)
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = pair->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
@ -1048,7 +1059,7 @@ TEST(PairStyle, single)
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto prerequisite : test_config.prerequisites) {
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
test_config.prerequisites.pop_back();
@ -1130,11 +1141,7 @@ TEST(PairStyle, single)
command("atom_modify map array");
command("region box block -10.0 10.0 -10.0 10.0 -10.0 10.0 units box");
char buf[10];
snprintf(buf, 10, "%d", ntypes);
std::string cmd("create_box ");
cmd += buf;
cmd += " box";
auto cmd = fmt::format("create_box {} box", ntypes);
if (molecular) {
cmd += " bond/types 1"
" extra/bond/per/atom 1"
@ -1304,7 +1311,7 @@ TEST(PairStyle, extract)
GTEST_SKIP();
}
Pair *pair = lmp->force->pair;
auto pair = lmp->force->pair;
if (!pair->compute_flag) {
std::cerr << "Pair style disabled" << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();

78
unittest/force-styles/tests/angle-charmm.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:19 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 46.1 111.3 0.0 0.000
3 40.0 120.0 35.0 2.410
4 33.0 108.5 30.0 2.163
equilibrium: 4 1.92161 1.94255 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9425514574696887 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 85.4248638845977
init_stress: ! |2-
1.8143089201050887e+02 -4.4008327668528100e+00 1.1809359848490450e+02 1.3470039754098281e+02 9.3127587748087279e+01 2.3868960580224421e+01
init_forces: ! |2
21 1.5269813353706816e+00 1.9115283296031365e+00 -5.7126680835892021e+00
22 -2.4212822369319898e+01 -1.1732635537541306e+01 -7.1373318326447102e+00
23 2.2685841033949217e+01 9.8211072079381694e+00 1.2849999916233912e+01
19 -1.8729001948214922e+01 -1.6361947190261777e+01 -3.2134590021289293e+00
18 7.0507994374434446e-02 7.3680637947826888e-01 -2.9901987340388825e+00
20 1.8658493953840487e+01 1.5625140810783508e+01 6.2036577361678118e+00
28 -2.1397316777571888e+01 -6.8536308873550515e+00 -1.0104593869135021e+01
1 3.8386618977092809e+01 9.2563644890222108e+00 -2.2416069655629478e+01
2 4.8047222128896552e+00 5.8908874219218736e+00 -3.6078250436995862e+00
3 2.6714408920784543e+00 -2.3742017076932243e-02 2.1100086635874408e+01
4 -1.9280446193919857e+01 -1.0907565986617040e+01 -2.0121340659982309e+01
5 -1.8343508172093760e+01 -4.1071023429215984e+01 1.6108594011594683e+01
6 2.1238309901668043e+01 5.7121253219257824e+00 -1.6787970380345595e+01
7 -2.5311264980599468e+01 1.9532283354226724e+01 -2.4286994823128929e+01
8 1.0452003565543395e+01 -2.3201291666991558e+01 9.0068263361646899e+01
9 -1.5916624143704812e+01 1.6483610301406415e+01 -4.1516194400253736e-01
10 1.5262370040243479e+01 1.7209374979747956e+01 -5.0097168024346068e+01
11 -2.1025039799233362e+01 -6.8138721666064477e+00 9.3257489337892920e+00
12 -3.7942492100969893e+00 -1.8949256479033437e+01 7.2924357616797710e+00
13 2.6829248438599908e+01 -1.8477615701199301e+01 7.6270643598239811e+00
14 -9.1419604634794620e+00 -5.8258733174381518e+00 -3.5139934203515040e+01
3 2.6714408920784543e+00 -2.3742017076932243e-02 2.1100086635874408e+01
6 2.1238309901668043e+01 5.7121253219257824e+00 -1.6787970380345595e+01
7 -2.5311264980599468e+01 1.9532283354226724e+01 -2.4286994823128929e+01
15 -3.9745927947694284e+00 2.5196516981363281e+01 3.2110867442129567e+01
8 1.0452003565543395e+01 -2.3201291666991558e+01 9.0068263361646899e+01
9 -1.5916624143704812e+01 1.6483610301406415e+01 -4.1516194400253736e-01
16 -2.9503839293712968e+00 2.5409363689785007e+01 -7.2255876751122914e+00
17 9.3355659152692783e-02 5.7971422477959977e-01 -3.5350080967767701e+00
5 -1.8343508172093760e+01 -4.1071023429215984e+01 1.6108594011594683e+01
13 2.6829248438599908e+01 -1.8477615701199301e+01 7.6270643598239811e+00
2 4.8047222128896552e+00 5.8908874219218736e+00 -3.6078250436995862e+00
1 3.8386618977092809e+01 9.2563644890222108e+00 -2.2416069655629478e+01
27 -1.2828590583680111e-01 1.0531267905268624e+00 -3.5872993954368049e-01
29 2.1525602683408689e+01 5.8005040968281891e+00 1.0463323808678702e+01
18 7.0507994374434446e-02 7.3680637947826888e-01 -2.9901987340388825e+00
19 -1.8729001948214922e+01 -1.6361947190261777e+01 -3.2134590021289293e+00
20 1.8658493953840487e+01 1.5625140810783508e+01 6.2036577361678118e+00
21 1.5269813353706816e+00 1.9115283296031365e+00 -5.7126680835892021e+00
22 -2.4212822369319898e+01 -1.1732635537541306e+01 -7.1373318326447102e+00
23 2.2685841033949217e+01 9.8211072079381694e+00 1.2849999916233912e+01
24 -5.8307622758841404e-01 2.2664518498581661e+00 -1.3493584963979171e+00
25 -1.9566415223447844e+01 -1.2547949048865153e+01 -1.0241193948074248e+01
26 2.0149491451036258e+01 1.0281497199006987e+01 1.1590552444472165e+01
27 -1.2828590583680111e-01 1.0531267905268624e+00 -3.5872993954368049e-01
28 -2.1397316777571888e+01 -6.8536308873550515e+00 -1.0104593869135021e+01
29 2.1525602683408689e+01 5.8005040968281891e+00 1.0463323808678702e+01
run_energy: 69.5038576349246
run_stress: ! |2-
1.5649327850389238e+02 -1.3576175184752444e+01 1.0301817481047499e+02 1.1751125350905258e+02 8.1820504826714767e+01 8.0309752683500211e+00
run_forces: ! |2
21 -1.4384266302963056e-01 -1.6712728564325374e-01 5.3093449084065192e-01
22 -1.9343247281638671e+01 -8.6574192096222582e+00 -8.4047349351069993e+00
23 1.9487089944668302e+01 8.8245464952655119e+00 7.8738004442663474e+00
19 -1.4296841483844430e+01 -1.2025900714259519e+01 -5.1480379176678346e+00
18 -1.1328653272278899e-01 -8.7030074096365340e-01 3.4079850166128001e+00
20 1.4410128016567219e+01 1.2896201455223173e+01 1.7400529010550347e+00
28 -1.9195019940436467e+01 -4.6371717881364969e+00 -9.5643824275161027e+00
1 3.2673907043103924e+01 7.0945689163394468e+00 -1.8445622162375827e+01
2 3.9740242751610664e+00 2.9513087966460372e+00 -5.0029928500601795e+00
3 7.2187270355452906e+00 -5.9092128037891003e+00 1.4203606972280422e+01
4 -1.6927467901050289e+01 -7.3859651827093025e+00 -1.4353585997401646e+01
5 -1.8409024900834989e+01 -3.4535581103141681e+01 1.3272518754203558e+01
6 2.0589410812493110e+01 8.0236562189313609e+00 -1.2960642418999164e+01
7 -2.3631931177375314e+01 1.8664083313377326e+01 -2.1460676242173019e+01
8 4.4078064602776070e+00 -1.9506406597487576e+01 7.6157986021827725e+01
9 -1.2872279366933459e+01 1.3367415437083203e+01 -6.7987510304161081e-01
10 1.7068495816883917e+01 1.3277171419237666e+01 -3.6716828531348568e+01
11 -2.0022241908167199e+01 -4.3872495528933699e+00 8.3275988802544596e+00
12 -7.7453219525172825e+00 -1.8894522494274831e+01 9.0662328749664240e+00
13 2.2164198238442463e+01 -1.6052737131589645e+01 7.1273217580409165e+00
14 -5.1588905300387884e+00 -1.8946152907089644e+00 -2.9531709636198215e+01
3 7.2187270355452906e+00 -5.9092128037891003e+00 1.4203606972280422e+01
6 2.0589410812493110e+01 8.0236562189313609e+00 -1.2960642418999164e+01
7 -2.3631931177375314e+01 1.8664083313377326e+01 -2.1460676242173019e+01
15 -2.5742212978495180e+00 2.1122073440175640e+01 2.4271434448540585e+01
8 4.4078064602776070e+00 -1.9506406597487576e+01 7.6157986021827725e+01
9 -1.2872279366933459e+01 1.3367415437083203e+01 -6.7987510304161081e-01
16 -3.5711419901429564e-01 2.2624935653043305e+01 -8.4643921759749290e+00
17 -3.9807644812623544e-01 1.4410769617604862e+00 -4.8103745925409314e+00
5 -1.8409024900834989e+01 -3.4535581103141681e+01 1.3272518754203558e+01
13 2.2164198238442463e+01 -1.6052737131589645e+01 7.1273217580409165e+00
2 3.9740242751610664e+00 2.9513087966460372e+00 -5.0029928500601795e+00
1 3.2673907043103924e+01 7.0945689163394468e+00 -1.8445622162375827e+01
27 2.7630957147703228e-01 -2.0949168656441595e+00 6.7238481135276018e-01
29 1.8918710368959434e+01 6.7320886537806564e+00 8.8919976161633425e+00
18 -1.1328653272278899e-01 -8.7030074096365340e-01 3.4079850166128001e+00
19 -1.4296841483844430e+01 -1.2025900714259519e+01 -5.1480379176678346e+00
20 1.4410128016567219e+01 1.2896201455223173e+01 1.7400529010550347e+00
21 -1.4384266302963056e-01 -1.6712728564325374e-01 5.3093449084065192e-01
22 -1.9343247281638671e+01 -8.6574192096222582e+00 -8.4047349351069993e+00
23 1.9487089944668302e+01 8.8245464952655119e+00 7.8738004442663474e+00
24 6.6099237575914671e-01 -2.5342427128367895e+00 1.4932164263150582e+00
25 -1.7526054501171469e+01 -8.8950231017495049e+00 -1.0437094403998735e+01
26 1.6865062125412322e+01 1.1429265814586294e+01 8.9438779776836768e+00
27 2.7630957147703228e-01 -2.0949168656441595e+00 6.7238481135276018e-01
28 -1.9195019940436467e+01 -4.6371717881364969e+00 -9.5643824275161027e+00
29 1.8918710368959434e+01 6.7320886537806564e+00 8.8919976161633425e+00
...

78
unittest/force-styles/tests/angle-class2.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:19 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -21,73 +21,73 @@ angle_coeff: ! |
1 ba 20.0 0.0 1.5 1.5
3 ba 10.0 10.0 1.5 1.5
4 ba 0.0 20.0 1.5 1.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 45.6315872862689
init_stress: ! |2-
1.0380900034455654e+02 -8.5596888576343744e+01 1.0543371457027396e+01 9.3533772092305199e+01 -3.0453078736699425e+01 1.6197471265279837e+00
init_forces: ! |2
21 3.9487378529081880e+00 4.3175316427012014e+00 -1.1481919601133793e+01
22 -6.5477089696018744e+00 -4.1918690971369452e+00 3.4304260006102911e+00
23 2.5989711166936864e+00 -1.2566254556425660e-01 8.0514936005235018e+00
19 -2.0533806941129176e+00 -2.3525964439530416e+00 2.1320670955883561e+00
18 4.7908728028679270e-01 1.6800089801308631e+00 -5.5268875505867383e+00
20 1.5742934138261249e+00 6.7258746382217860e-01 3.3948204549983823e+00
28 -7.9798149428972343e-01 -1.3623378004463826e+00 -7.5274691791676882e-02
1 4.7202113476907201e+01 9.2452097148049379e+00 -2.1894202744712533e+01
2 -1.7062797644104073e+00 -1.3815331678107317e+01 -1.1109216556988997e+01
3 -1.0818552868961547e+01 4.2757153900854306e+01 4.0134050204129267e+01
4 -1.6107291199158311e+01 -2.0450831607561582e+01 1.2394641799374179e+01
5 -4.1997303662023540e+01 -4.1453062742803219e+01 -1.7536792897035419e+01
6 5.6639792403457349e+01 -1.3580769610788053e+01 -3.9712060060785255e+01
7 -1.8054439727078506e+01 1.6983062508083172e+01 1.5587306726806713e+00
8 -1.0525801597483865e+01 -1.5574411954009244e+01 8.4303126221362277e+01
9 -1.4606126670427546e+01 1.7088847325775880e+01 3.5265027966992148e+00
10 -9.2168170333014618e+00 2.5310906045489432e+01 -6.6219876033939016e+01
11 -2.0537012066379056e+01 -7.0930129287428976e+00 7.5068656204459945e+00
12 -2.8436344574011141e-01 -6.5767250423083183e+00 -7.8126221608778286e+00
13 3.1055904718024561e+00 8.1431271170459514e+00 -1.2597779054058647e+00
14 1.6321646299623836e+01 -6.4737292023940052e+00 -6.0969666237587319e+00
3 -1.0818552868961547e+01 4.2757153900854306e+01 4.0134050204129267e+01
6 5.6639792403457349e+01 -1.3580769610788053e+01 -3.9712060060785255e+01
7 -1.8054439727078506e+01 1.6983062508083172e+01 1.5587306726806713e+00
15 1.2014703003264437e+01 -4.7819952969181587e+00 1.5497667618539472e+01
8 -1.0525801597483865e+01 -1.5574411954009244e+01 8.4303126221362277e+01
9 -1.4606126670427546e+01 1.7088847325775880e+01 3.5265027966992148e+00
16 9.3845211462413065e+00 9.2380044230210405e+00 6.9332654848904189e+00
17 -8.1437876633224571e-01 1.0335590285580882e+00 -2.1333543461785509e-01
5 -4.1997303662023540e+01 -4.1453062742803219e+01 -1.7536792897035419e+01
13 3.1055904718024561e+00 8.1431271170459514e+00 -1.2597779054058647e+00
2 -1.7062797644104073e+00 -1.3815331678107317e+01 -1.1109216556988997e+01
1 4.7202113476907201e+01 9.2452097148049379e+00 -2.1894202744712533e+01
27 -1.3120258950869723e-01 2.3248353742613195e+00 -7.0687277526256109e-01
29 9.2918408379842066e-01 -9.6249757381493684e-01 7.8214746705423799e-01
18 4.7908728028679270e-01 1.6800089801308631e+00 -5.5268875505867383e+00
19 -2.0533806941129176e+00 -2.3525964439530416e+00 2.1320670955883561e+00
20 1.5742934138261249e+00 6.7258746382217860e-01 3.3948204549983823e+00
21 3.9487378529081880e+00 4.3175316427012014e+00 -1.1481919601133793e+01
22 -6.5477089696018744e+00 -4.1918690971369452e+00 3.4304260006102911e+00
23 2.5989711166936864e+00 -1.2566254556425660e-01 8.0514936005235018e+00
24 -8.4094048868779181e-01 4.6838060982897600e+00 -2.5056979703433946e+00
25 -1.3589399152326838e+00 -3.2194810517526529e+00 2.1726606908305435e-01
26 2.1998804039204756e+00 -1.4643250465371074e+00 2.2884319012603402e+00
27 -1.3120258950869723e-01 2.3248353742613195e+00 -7.0687277526256109e-01
28 -7.9798149428972343e-01 -1.3623378004463826e+00 -7.5274691791676882e-02
29 9.2918408379842066e-01 -9.6249757381493684e-01 7.8214746705423799e-01
run_energy: 34.7710094271953
run_stress: ! |2-
8.2599011234487151e+01 -7.3165139178918366e+01 1.3818327814911246e+01 6.3916212989349248e+01 -3.2786151147810777e+01 -1.4139354495141657e+01
run_forces: ! |2
21 7.2982701997905797e-01 7.4575563779175358e-01 -2.1049026413553120e+00
22 -1.1629868443291469e+00 -7.2090297774647027e-01 6.5350153907281450e-01
23 4.3315982435008887e-01 -2.4852660045283331e-02 1.4514011022824975e+00
19 1.2218057627151511e+00 1.4528878204712177e+00 -1.4511972616407449e+00
18 -2.9253358773418248e-01 -1.0692065587751192e+00 3.5574890115063189e+00
20 -9.2927217498096859e-01 -3.8368126169609845e-01 -2.1062917498655742e+00
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29 1.3637404946955267e-01 -1.4167336782347603e-01 1.1115177578341261e-01
...

78
unittest/force-styles/tests/angle-cosine.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:19:48 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0
3 50.0
4 100.0
equilibrium: 4 3.14159 3.14159 3.14159 3.14159
equilibrium: 4 3.141592653589793 3.141592653589793 3.141592653589793 3.141592653589793
extract: ! ""
natoms: 29
init_energy: 1347.86708569396
init_stress: ! |2-
9.7042018787767176e+01 -4.8524910053092775e+01 -4.8517108734674437e+01 2.1991310128767722e+02 1.5350601447035655e+02 4.9763634294547245e+01
init_forces: ! |2
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22 -5.0127223013422530e+01 -3.4176713950473413e+01 3.7229939541731568e+01
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29 4.1966200036026713e+01 -4.3470789503612323e+01 3.5325354396826512e+01
run_energy: 1244.44896829426
run_stress: ! |2-
7.4057360277435123e+01 -3.8153851541957792e+01 -3.5903508735477303e+01 1.8861542221783722e+02 1.1365123094061245e+02 4.5042317928787789e+01
run_forces: ! |2
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22 -4.3942601855226357e+01 -2.9895567644474593e+01 4.0574906186582929e+01
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29 3.6548693555942364e+01 -4.5118794315077615e+01 3.1421520699793842e+01
...

78
unittest/force-styles/tests/angle-cosine_delta.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:25:07 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 111.0
3 50.0 120.0
4 100.0 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 20.6509813301781
init_stress: ! |2-
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init_forces: ! |2
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29 2.0153217887603549e+00 -2.0875759345863187e+00 1.6964117873548172e+00
run_energy: 18.2003409008082
run_stress: ! |2-
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run_forces: ! |2
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27 -5.4153121699149231e-01 4.1113464239260065e+00 -1.3188046982828696e+00
29 1.5856308992507184e+00 -1.6556045883532153e+00 1.2943013674783828e+00
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26 1.4570265707370762e+00 -1.0129523972916150e+00 1.5394511081284161e+00
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29 1.5856308992507184e+00 -1.6556045883532153e+00 1.2943013674783828e+00
...

78
unittest/force-styles/tests/angle-cosine_periodic.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:27:17 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 1 2
3 50.0 -1 3
4 100.0 -1 4
equilibrium: 4 3.14159 3.14159 3.14159 3.14159
equilibrium: 4 3.141592653589793 3.141592653589793 3.141592653589793 3.141592653589793
extract: ! ""
natoms: 29
init_energy: 946.676664091363
init_stress: ! |2-
3.8581448829084906e+00 -6.3926599144452858e+01 6.0068454261544439e+01 1.4347370855129017e+02 1.0109551149053127e+02 4.9470344115369670e+01
init_forces: ! |2
21 1.6243294930835876e+01 2.0333921382774719e+01 -6.0768622624445221e+01
22 -2.8924589352090472e+01 -1.9720769613680826e+01 2.1482552755004811e+01
23 1.2681294421254595e+01 -6.1315176909389102e-01 3.9286069869440411e+01
19 -2.0180190840279820e+01 -2.5140421523544326e+01 2.9933594625645306e+01
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20 1.8532057187109345e+01 7.9174753787429015e+00 3.9962694539321184e+01
28 -1.9235439225569891e+01 -4.3179911322776611e+01 1.0030656861974458e+00
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2 4.6997439470662350e+00 3.8052682089524090e+01 3.0599010994189470e+01
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5 2.7634466780141157e+01 1.5504150132065057e+01 1.0078115065618357e+01
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16 -7.0395776185793807e+01 4.3227686209287491e+01 3.0567216126495769e+01
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20 1.8532057187109345e+01 7.9174753787429015e+00 3.9962694539321184e+01
21 1.6243294930835876e+01 2.0333921382774719e+01 -6.0768622624445221e+01
22 -2.8924589352090472e+01 -1.9720769613680826e+01 2.1482552755004811e+01
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27 -8.7971258084923178e+00 7.2217511410368814e+01 -2.4599681382405976e+01
28 -1.9235439225569891e+01 -4.3179911322776611e+01 1.0030656861974458e+00
29 2.8032565034062209e+01 -2.9037600087592210e+01 2.3596615696208531e+01
run_energy: 898.669772734792
run_stress: ! |2-
3.3936204372603932e+01 -7.2755211808629142e+01 3.8819007436025174e+01 1.6151069358014291e+02 1.1122271842942311e+02 8.3043098226366141e+01
run_forces: ! |2
21 2.3973304149122125e+01 2.7715634331495849e+01 -8.8261932917781166e+01
22 -3.8201692739909106e+01 -2.5640471620503025e+01 3.3028167998478402e+01
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20 2.1504448880273543e+01 7.6775744632130341e+00 5.4070161419453484e+01
28 -2.1142754917126503e+01 -5.6779623821268707e+01 2.1680211853374161e+00
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29 3.4039779271821835e+01 -3.9883907026795981e+01 2.8782091767445245e+01
...

78
unittest/force-styles/tests/angle-cosine_shift.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:46:58 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 111.0
3 50.0 120.0
4 100.0 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457567 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: -2039.67450933491
init_stress: ! |2-
2.2236590310678018e+01 -2.1731920007845627e+01 -5.0467030283239134e-01 2.2818792439800895e+01 -6.9536967934807379e+00 -2.1412469755446228e-01
init_forces: ! |2
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22 -1.5210327846109488e+00 -1.0370393423753146e+00 1.1296847343187952e+00
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20 4.4367624168644504e-01 1.8955238936609081e-01 9.5674743186107480e-01
28 -1.5699617393892926e-01 -3.5242662198670610e-01 8.1868406068466293e-03
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4 -3.9947027489528111e+00 -6.1291802260361044e+00 3.2084116555510889e+00
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13 7.2062529217331339e-01 1.8229082041071101e+00 -2.6515752312201046e-02
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3 -1.4228732558899586e+00 1.3162676416500810e+01 1.2811665774003211e+01
6 1.1673784825051111e+01 -2.3568912782672986e+00 -8.0390840557244125e+00
7 -4.0343336515091934e+00 3.5987946950438578e+00 -8.7899903829119208e-01
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27 -7.1800548840952522e-02 5.8942625899320822e-01 -2.0077814766093691e-01
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run_stress: ! |2-
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29 5.2512815378793903e-02 -5.4435647949418853e-02 4.2773538009412027e-02
...

78
unittest/force-styles/tests/angle-cosine_shift_exp.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:50:49 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 111.0 -1.2
3 50.0 120.0 1.5
4 100.0 108.5 -0.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457567 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: -2037.74792247299
init_stress: ! |2-
3.1544969690090625e+01 -4.0852408597894950e+01 9.3074389078043254e+00 2.4930817297140411e+01 -4.2843599056057773e+00 5.4955553986615975e+00
init_forces: ! |2
21 1.9723953889780230e+00 2.4691131292019586e+00 -7.3790294130202927e+00
22 -3.5122631774568323e+00 -2.3946591635962085e+00 2.6085894627826085e+00
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29 5.2918694209942296e-01 -5.4815957004246063e-01 4.4544696102546910e-01
run_energy: -2039.29043001045
run_stress: ! |2-
2.3409626405776471e+01 -3.7232961535901836e+01 1.3823335130125358e+01 1.8449759086855384e+01 -7.3488270840678744e+00 -3.1148137591843422e-01
run_forces: ! |2
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22 -9.6651487888787813e-01 -6.3588254799908128e-01 7.5512929355341774e-01
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29 7.8008757316469682e-02 -8.0939837604843634e-02 6.3558008978471400e-02
...

78
unittest/force-styles/tests/angle-cosine_squared.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 18:51:42 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 111.0
3 50.0 120.0
4 100.0 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 36.0116244857696
init_stress: ! |2-
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init_forces: ! |2
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...

78
unittest/force-styles/tests/angle-fourier.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 19:00:31 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 0.5 0.0 0.5
3 50.0 0.0 0.0 1.0
4 100.0 0.3 0.3 0.3
equilibrium: 4 3.14159 1.5708 1.5708 1.82348
equilibrium: 4 3.141592653589793 1.5707963267948966 1.5707963267948966 1.8234765819369754
extract: ! ""
natoms: 29
init_energy: 400.840366320102
init_stress: ! |-
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78
unittest/force-styles/tests/angle-fourier_simple.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 19:03:15 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 1.0 2.0
3 50.0 1.0 3.0
4 100.0 -0.5 1.5
equilibrium: 4 3.14159 1.5708 1.0472 2.0944
equilibrium: 4 3.141592653589793 1.5707963267948966 1.0471975511965976 2.0943951023931953
extract: ! ""
natoms: 29
init_energy: 2474.07480135906
init_stress: ! |-
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init_forces: ! |2
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run_stress: ! |2-
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run_forces: ! |2
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29 -4.6952450851048468e+01 4.0843882895284516e+01 -3.6419735991490157e+01
...

78
unittest/force-styles/tests/angle-harmonic.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:20 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 45.0 111.0
3 50.0 120.0
4 100.0 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 41.530817896491
init_stress: ! |2-
8.9723357320869255e+01 -8.7188643750026529e+01 -2.5347135708427588e+00 9.2043419883119697e+01 -2.8187238090404989e+01 -1.5291148024927028e+00
init_forces: ! |2
21 3.4186149299343622e+00 4.2795410364249307e+00 -1.2789555411020601e+01
22 -6.0875600315279446e+00 -4.1504951869796436e+00 4.5212856070195588e+00
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19 -1.9328033033421517e+00 -2.4078805870919515e+00 2.8669575541313312e+00
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20 1.7749495845934198e+00 7.5831406587194772e-01 3.8275172235676602e+00
28 -6.2799575211499037e-01 -1.4097313073755557e+00 3.2747938980615732e-02
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18 1.5785371874873189e-01 1.6495665212200037e+00 -6.6944747776989910e+00
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20 1.7749495845934198e+00 7.5831406587194772e-01 3.8275172235676602e+00
21 3.4186149299343622e+00 4.2795410364249307e+00 -1.2789555411020601e+01
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28 -6.2799575211499037e-01 -1.4097313073755557e+00 3.2747938980615732e-02
29 9.1520300398842180e-01 -9.4801523858010661e-01 7.7037879134105569e-01
run_energy: 29.2286477697792
run_stress: ! |2-
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run_forces: ! |2
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22 -1.0299517357238845e+00 -6.7850914711871291e-01 8.1029011311054200e-01
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1 3.6220193547187421e+01 1.1585587142479543e+01 -1.7238241972840832e+01
27 -1.4554421797154906e-02 1.1056084388051551e-01 -3.5467198058544314e-02
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29 4.2812328190663218e-02 -4.4471254485253520e-02 3.4893068510691336e-02
...

78
unittest/force-styles/tests/angle-hybrid.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 19:08:46 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -15,73 +15,73 @@ angle_coeff: ! |
2 cosine/shift 45.0 111.0
3 cosine/shift 50.0 120.0
4 harmonic 100.0 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: -669.446517131318
init_stress: ! |2-
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init_forces: ! |2
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28 -6.2799575211499037e-01 -1.4097313073755557e+00 3.2747938980615732e-02
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run_energy: -678.497727741936
run_stress: ! |2-
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run_forces: ! |2
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29 4.2812328190663218e-02 -4.4471254485253520e-02 3.4893068510691336e-02
...

78
unittest/force-styles/tests/angle-quartic.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 21:09:28 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 111.0 45.0 -5.0 2.0
3 120.0 50.0 -9.5 -1.5
4 108.5 100.0 5.0 -2.0
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 41.0458477552901
init_stress: ! |2-
8.9219936238979074e+01 -8.4659896678146225e+01 -4.5600395608328208e+00 9.1474094820946405e+01 -2.5970677094019297e+01 -1.7436792207668637e+00
init_forces: ! |2
21 3.3782476603682650e+00 4.2290078847897892e+00 -1.2638535351292170e+01
22 -6.0156776517253148e+00 -4.1014858187180927e+00 4.4678979167928112e+00
23 2.6374299913570498e+00 -1.2752206607169603e-01 8.1706374344993584e+00
19 -1.9216019382035907e+00 -2.3939259598314173e+00 2.8503423929584120e+00
18 1.5693889356236790e-01 1.6400066260705177e+00 -6.6556776293982676e+00
20 1.7646630446412228e+00 7.5391933376089948e-01 3.8053352364398561e+00
28 -6.2670131824814423e-01 -1.4068255489507977e+00 3.2680438458290273e-02
1 4.8022594085382373e+01 7.4684610857333489e+00 -3.1585942438177707e+01
2 -1.1172658072754227e+00 -9.0462291249476792e+00 -7.2742747488602291e+00
3 -6.5649615969867270e+00 5.1788140345142175e+01 5.0352071932004861e+01
4 -1.6179136028073493e+01 -2.4462875151875991e+01 1.3137258098814669e+01
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18 1.5693889356236790e-01 1.6400066260705177e+00 -6.6556776293982676e+00
19 -1.9216019382035907e+00 -2.3939259598314173e+00 2.8503423929584120e+00
20 1.7646630446412228e+00 7.5391933376089948e-01 3.8053352364398561e+00
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29 9.1331657440762881e-01 -9.4606117594995109e-01 7.6879087550810066e-01
run_energy: 29.1502240990426
run_stress: ! |2-
6.7042207793770658e+01 -7.3107350065369147e+01 6.0651422715984635e+00 5.7540451643703122e+01 -2.5791549664995877e+01 -1.5308659267071452e+01
run_forces: ! |2
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22 -1.0420455963088935e+00 -6.8645646043483677e-01 8.1967897514834509e-01
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18 -1.1728343467585933e-01 -8.9608593127973857e-01 3.5063388996752507e+00
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5 -3.5082415370053397e+01 -3.4273036378440537e+01 -2.0798846041201188e+01
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1 3.6505789840992350e+01 1.1382172519452340e+01 -1.6875444601860664e+01
27 -1.4670545669870434e-02 1.1144302048037638e-01 -3.5750197695858035e-02
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29 4.3154075129372728e-02 -4.4826053131538646e-02 3.5171557086110666e-02
...

78
unittest/force-styles/tests/angle-table_linear.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 2 Jun 2020
date_generated: Sun Jun 14 14:43:01 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 ${input_dir}/angle_table.txt harmonic_2
3 ${input_dir}/angle_table.txt harmonic_3
4 ${input_dir}/angle_table.txt harmonic_4
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 41.5339263499027
init_stress: ! |2-
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init_forces: ! |2
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3 -5.9057050592858733e+00 5.3263619873546141e+01 5.2353380124691299e+01
6 4.7083124388174781e+01 -9.5212933434476099e+00 -3.2526392870546793e+01
7 -1.6208182775476292e+01 1.4458587960739091e+01 -3.5314745459502683e+00
15 1.2402914209534778e+01 -6.2644630791613931e+00 1.8484576795819923e+01
8 -6.5664612141880756e+00 -2.5126850154274244e+01 8.2187944731423272e+01
9 -1.5504395262358333e+01 1.6121044185227852e+01 -4.2007069622478133e-01
16 3.8927757686510400e-01 1.0690061587911154e+01 6.1542759189377394e+00
17 1.4664194297570774e+00 -1.9971277376602408e+00 1.0776844613215992e+00
5 -4.4802331573497604e+01 -4.8300919461089265e+01 -2.3310767889219282e+01
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19 -1.9328033033421668e+00 -2.4078805870919702e+00 2.8669575541313530e+00
20 1.7749495845934335e+00 7.5831406587195360e-01 3.8275172235676891e+00
21 3.4186149299343822e+00 4.2795410364249564e+00 -1.2789555411020675e+01
22 -6.0875600315279801e+00 -4.1504951869796685e+00 4.5212856070195855e+00
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24 -1.3053945393770572e+00 5.0741459325183218e+00 -3.0209518576072987e+00
25 -1.0471133765834273e+00 -3.5082261409793825e+00 5.7374874908501183e-01
26 2.3525079159604845e+00 -1.5659197915389398e+00 2.4472031085222867e+00
27 -2.8720725187343266e-01 2.3577465459556737e+00 -8.0312673032167514e-01
28 -6.2799575211499314e-01 -1.4097313073755624e+00 3.2747938980615898e-02
29 9.1520300398842580e-01 -9.4801523858011116e-01 7.7037879134105924e-01
run_energy: 29.2317863480852
run_stress: ! |2-
6.7161703985479718e+01 -7.4680138065367359e+01 7.5184340798876548e+00 5.7521437901240908e+01 -2.7304190748521801e+01 -1.4932945649428691e+01
run_forces: ! |2
21 6.0524643645662701e-01 7.0314728523699266e-01 -2.2349906198624625e+00
22 -1.0299517357238868e+00 -6.7850914711871446e-01 8.1029011311054377e-01
23 4.2470529926725969e-01 -2.4638138118278197e-02 1.4247005067519189e+00
19 9.8256914435042142e-01 1.2515894863018673e+00 -1.5372413162209075e+00
18 -1.1709942604030243e-01 -8.9468235295759790e-01 3.5008479949198064e+00
20 -8.6546971831011899e-01 -3.5690713334426938e-01 -1.9636066786988988e+00
28 -2.8257906393443971e-02 -6.6089589395111600e-02 5.7412954785172193e-04
1 3.6220193547187456e+01 1.1585587142479525e+01 -1.7238241972840854e+01
2 -1.7637583558697996e+00 -1.3758538851839569e+01 -1.1469071109412802e+01
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5 -3.5092143924598346e+01 -3.4761325046913385e+01 -2.1062123798094682e+01
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7 -1.4366916728367732e+01 1.3135040103127022e+01 -3.0387136809768114e+00
8 -8.5333281419768152e+00 -2.4737111100998341e+01 6.5176870591189896e+01
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8 -8.5333281419768152e+00 -2.4737111100998341e+01 6.5176870591189896e+01
9 -1.2996571868203626e+01 1.3674206710496637e+01 -6.7871105914534136e-01
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5 -3.5092143924598346e+01 -3.4761325046913385e+01 -2.1062123798094682e+01
13 7.7658418286979858e-01 2.0512357329016981e+00 1.8932242747136030e+00
2 -1.7637583558697996e+00 -1.3758538851839569e+01 -1.1469071109412802e+01
1 3.6220193547187456e+01 1.1585587142479525e+01 -1.7238241972840854e+01
27 -1.4554421797121797e-02 1.1056084388026395e-01 -3.5467198058463670e-02
29 4.2812328190565768e-02 -4.4471254485152351e-02 3.4893068510611948e-02
18 -1.1709942604030243e-01 -8.9468235295759790e-01 3.5008479949198064e+00
19 9.8256914435042142e-01 1.2515894863018673e+00 -1.5372413162209075e+00
20 -8.6546971831011899e-01 -3.5690713334426938e-01 -1.9636066786988988e+00
21 6.0524643645662701e-01 7.0314728523699266e-01 -2.2349906198624625e+00
22 -1.0299517357238868e+00 -6.7850914711871446e-01 8.1029011311054377e-01
23 4.2470529926725969e-01 -2.4638138118278197e-02 1.4247005067519189e+00
24 4.1516966455942839e-01 -1.5912776575034653e+00 9.3767616296742518e-01
25 3.0070697634260080e-01 1.0957067953103117e+00 -1.8209981159009125e-01
26 -7.1587664090202918e-01 4.9557086219315349e-01 -7.5557635137733392e-01
27 -1.4554421797121797e-02 1.1056084388026395e-01 -3.5467198058463670e-02
28 -2.8257906393443971e-02 -6.6089589395111600e-02 5.7412954785172193e-04
29 4.2812328190565768e-02 -4.4471254485152351e-02 3.4893068510611948e-02
...

78
unittest/force-styles/tests/angle-table_spline.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 2 Jun 2020
date_generated: Sun Jun 14 14:43:02 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 ${input_dir}/angle_table.txt harmonic_2
3 ${input_dir}/angle_table.txt harmonic_3
4 ${input_dir}/angle_table.txt harmonic_4
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 41.530817896491
init_stress: ! |2-
8.9723357320869255e+01 -8.7188643750026586e+01 -2.5347135708426856e+00 9.2043419883119654e+01 -2.8187238090404925e+01 -1.5291148024925465e+00
init_forces: ! |2
21 3.4186149299343822e+00 4.2795410364249564e+00 -1.2789555411020675e+01
22 -6.0875600315279801e+00 -4.1504951869796685e+00 4.5212856070195855e+00
23 2.6689451015935979e+00 -1.2904584944528774e-01 8.2682698040010898e+00
19 -1.9328033033421659e+00 -2.4078805870919697e+00 2.8669575541313526e+00
18 1.5785371874873277e-01 1.6495665212200161e+00 -6.6944747776990408e+00
20 1.7749495845934331e+00 7.5831406587195349e-01 3.8275172235676886e+00
28 -6.2799575211499314e-01 -1.4097313073755624e+00 3.2747938980615898e-02
1 4.7865489310693469e+01 7.8760925902181818e+00 -3.2694525514709696e+01
2 -1.1124882516177403e+00 -9.0075464203887918e+00 -7.2431691227364867e+00
3 -5.9057050592858733e+00 5.3263619873546141e+01 5.2353380124691299e+01
4 -1.6032230038990630e+01 -2.4560529343731371e+01 1.2891625920422312e+01
5 -4.4802331573497604e+01 -4.8300919461089265e+01 -2.3310767889219282e+01
6 4.7083124388174781e+01 -9.5212933434476028e+00 -3.2526392870546793e+01
7 -1.6208182775476288e+01 1.4458587960739088e+01 -3.5314745459502666e+00
8 -6.5664612141880756e+00 -2.5126850154274251e+01 8.2187944731423272e+01
9 -1.5504395262358333e+01 1.6121044185227852e+01 -4.2007069622478133e-01
10 9.9863759179365168e+00 4.1873540105704564e+01 -6.6085640966037303e+01
11 -2.0441876158908627e+01 -6.5186824168985842e+00 9.0023620309811001e+00
12 -1.0772126658369590e+01 -1.0807367300158258e+01 -9.6049647456797800e+00
13 2.8847886813946353e+00 7.2973241014859322e+00 -1.0414233993843336e-01
14 1.5267407478336397e+01 -9.4754911480231616e+00 -6.6307012925544209e+00
3 -5.9057050592858733e+00 5.3263619873546141e+01 5.2353380124691299e+01
6 4.7083124388174781e+01 -9.5212933434476028e+00 -3.2526392870546793e+01
7 -1.6208182775476288e+01 1.4458587960739088e+01 -3.5314745459502666e+00
15 1.2402914209534778e+01 -6.2644630791613913e+00 1.8484576795819923e+01
8 -6.5664612141880756e+00 -2.5126850154274251e+01 8.2187944731423272e+01
9 -1.5504395262358333e+01 1.6121044185227852e+01 -4.2007069622478133e-01
16 3.8927757686510400e-01 1.0690061587911154e+01 6.1542759189377394e+00
17 1.4664194297570774e+00 -1.9971277376602408e+00 1.0776844613215992e+00
5 -4.4802331573497604e+01 -4.8300919461089265e+01 -2.3310767889219282e+01
13 2.8847886813946353e+00 7.2973241014859322e+00 -1.0414233993843336e-01
2 -1.1124882516177403e+00 -9.0075464203887918e+00 -7.2431691227364867e+00
1 4.7865489310693469e+01 7.8760925902181818e+00 -3.2694525514709696e+01
27 -2.8720725187343266e-01 2.3577465459556737e+00 -8.0312673032167514e-01
29 9.1520300398842580e-01 -9.4801523858011116e-01 7.7037879134105924e-01
18 1.5785371874873277e-01 1.6495665212200161e+00 -6.6944747776990408e+00
19 -1.9328033033421659e+00 -2.4078805870919697e+00 2.8669575541313526e+00
20 1.7749495845934331e+00 7.5831406587195349e-01 3.8275172235676886e+00
21 3.4186149299343822e+00 4.2795410364249564e+00 -1.2789555411020675e+01
22 -6.0875600315279801e+00 -4.1504951869796685e+00 4.5212856070195855e+00
23 2.6689451015935979e+00 -1.2904584944528774e-01 8.2682698040010898e+00
24 -1.3053945393770572e+00 5.0741459325183218e+00 -3.0209518576072987e+00
25 -1.0471133765834273e+00 -3.5082261409793825e+00 5.7374874908501183e-01
26 2.3525079159604845e+00 -1.5659197915389398e+00 2.4472031085222867e+00
27 -2.8720725187343266e-01 2.3577465459556737e+00 -8.0312673032167514e-01
28 -6.2799575211499314e-01 -1.4097313073755624e+00 3.2747938980615898e-02
29 9.1520300398842580e-01 -9.4801523858011116e-01 7.7037879134105924e-01
run_energy: 29.2286477697792
run_stress: ! |2-
6.7161703985479718e+01 -7.4680138065367373e+01 7.5184340798876477e+00 5.7521437901240908e+01 -2.7304190748521808e+01 -1.4932945649428691e+01
run_forces: ! |2
21 6.0524643645662701e-01 7.0314728523699266e-01 -2.2349906198624625e+00
22 -1.0299517357238868e+00 -6.7850914711871446e-01 8.1029011311054377e-01
23 4.2470529926725969e-01 -2.4638138118278197e-02 1.4247005067519189e+00
19 9.8256914435042142e-01 1.2515894863018673e+00 -1.5372413162209075e+00
18 -1.1709942604030243e-01 -8.9468235295759790e-01 3.5008479949198064e+00
20 -8.6546971831011899e-01 -3.5690713334426938e-01 -1.9636066786988988e+00
28 -2.8257906393443971e-02 -6.6089589395111600e-02 5.7412954785172193e-04
1 3.6220193547187456e+01 1.1585587142479525e+01 -1.7238241972840854e+01
2 -1.7637583558697996e+00 -1.3758538851839569e+01 -1.1469071109412802e+01
3 -7.1131175159873807e+00 3.1523130842685656e+01 3.9133327910920080e+01
4 -1.1598618479874556e+01 -1.4069946914275876e+01 1.1631964860700624e+01
5 -3.5092143924598346e+01 -3.4761325046913385e+01 -2.1062123798094682e+01
6 4.3880849952881213e+01 -6.1732167988806470e+00 -2.6034788339533911e+01
7 -1.4366916728367732e+01 1.3135040103127022e+01 -3.0387136809768114e+00
8 -8.5333281419768152e+00 -2.4737111100998341e+01 6.5176870591189896e+01
9 -1.2996571868203626e+01 1.3674206710496637e+01 -6.7871105914534136e-01
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11 -1.9930599656448692e+01 -3.2836744898198695e+00 7.6150969595859648e+00
12 -5.8293065548538676e+00 -1.3423749355667578e+01 -5.2738511429384261e+00
13 7.7658418286979880e-01 2.0512357329016990e+00 1.8932242747136030e+00
14 1.2984672111772397e+01 -7.2763363322054886e-01 -4.8588140465034968e+00
3 -7.1131175159873807e+00 3.1523130842685656e+01 3.9133327910920080e+01
6 4.3880849952881213e+01 -6.1732167988806470e+00 -2.6034788339533911e+01
7 -1.4366916728367732e+01 1.3135040103127022e+01 -3.0387136809768114e+00
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8 -8.5333281419768152e+00 -2.4737111100998341e+01 6.5176870591189896e+01
9 -1.2996571868203626e+01 1.3674206710496637e+01 -6.7871105914534136e-01
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17 5.4695804680835325e-01 -7.5537048761029524e-01 4.0487452808956131e-01
5 -3.5092143924598346e+01 -3.4761325046913385e+01 -2.1062123798094682e+01
13 7.7658418286979880e-01 2.0512357329016990e+00 1.8932242747136030e+00
2 -1.7637583558697996e+00 -1.3758538851839569e+01 -1.1469071109412802e+01
1 3.6220193547187456e+01 1.1585587142479525e+01 -1.7238241972840854e+01
27 -1.4554421797121797e-02 1.1056084388026395e-01 -3.5467198058463670e-02
29 4.2812328190565768e-02 -4.4471254485152351e-02 3.4893068510611948e-02
18 -1.1709942604030243e-01 -8.9468235295759790e-01 3.5008479949198064e+00
19 9.8256914435042142e-01 1.2515894863018673e+00 -1.5372413162209075e+00
20 -8.6546971831011899e-01 -3.5690713334426938e-01 -1.9636066786988988e+00
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22 -1.0299517357238868e+00 -6.7850914711871446e-01 8.1029011311054377e-01
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24 4.1516966455942839e-01 -1.5912776575034653e+00 9.3767616296742518e-01
25 3.0070697634260080e-01 1.0957067953103117e+00 -1.8209981159009125e-01
26 -7.1587664090202918e-01 4.9557086219315349e-01 -7.5557635137733392e-01
27 -1.4554421797121797e-02 1.1056084388026395e-01 -3.5467198058463670e-02
28 -2.8257906393443971e-02 -6.6089589395111600e-02 5.7412954785172193e-04
29 4.2812328190565768e-02 -4.4471254485152351e-02 3.4893068510611948e-02
...

78
unittest/force-styles/tests/angle-zero.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:20 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 1e-14
prerequisites: ! |
atom full
@ -14,73 +14,73 @@ angle_coeff: ! |
2 111
3 120
4 108.5
equilibrium: 4 1.92161 1.93732 2.0944 1.89368
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
natoms: 29
init_energy: 0
init_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
init_forces: ! |2
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6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_energy: 0
run_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_forces: ! |2
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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...

6
unittest/force-styles/tests/atomic-pair-adp.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Tue May 26 18:05:10 202
epsilon: 5.0e-13
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:20 202
epsilon: 5e-13
prerequisites: ! |
pair adp
pre_commands: ! ""

6
unittest/force-styles/tests/atomic-pair-atm.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Tue May 26 18:19:54 202
epsilon: 5.0e-12
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:20 202
epsilon: 5e-12
prerequisites: ! |
pair atm
pre_commands: ! |

4
unittest/force-styles/tests/atomic-pair-beck.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Fri May 29 23:03:56 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-13
prerequisites: ! |
pair beck

136
unittest/force-styles/tests/atomic-pair-eam.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 12:25:55 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 6e-12
prerequisites: ! |
pair eam
@ -17,75 +17,75 @@ natoms: 32
init_vdwl: -368.582927487109
init_coul: 0
init_stress: ! |-
-3.9250135569982547e+02 -4.6446788990491922e+02 -4.1339651642483534e+02 1.9400736722937047e+01 1.1111963280257109e+00 1.2102392154667630e+01
-3.9250135569983178e+02 -4.6446788990492507e+02 -4.1339651642484176e+02 1.9400736722937040e+01 1.1111963280257418e+00 1.2102392154667420e+01
init_forces: ! |2
1 3.8702196239123237e+00 3.2087381358567679e+00 -3.2785146725168746e+00
2 1.5399659055502801e+00 5.3765327929110125e+00 1.5740005508928423e+00
3 9.6731722224674677e-01 -1.3144867798433710e+01 -9.0231732944261689e-01
4 -2.5073370343027146e+00 -5.2079180074533618e+00 -5.8913203171674402e+00
5 -2.8515169765266575e+00 7.6648779774003719e+00 -1.6135262802376316e+00
6 2.0428463056677254e-01 5.1885731021366555e+00 -5.9322347514392992e-01
7 -9.7176119399525651e-01 3.5285494740740462e+00 3.2284411698905560e+00
8 7.5364432092290201e-01 -5.2936287201396057e+00 -6.2408220629962896e+00
9 -5.8493861425957814e+00 -3.7463543270548563e+00 -3.9409131835960420e+00
10 -1.8023712766215385e+00 3.7006913245199451e+00 -3.8897352514951287e+00
11 3.5323555367973203e-01 -1.1327469434419406e+01 6.7182457803171030e+00
12 -4.4655507115633153e+00 -4.1270694194866087e+00 4.6918435871989708e+00
13 4.4725135751254337e+00 -3.8312677334791485e+00 -2.6917694312049267e-01
14 -2.7336352778320090e+00 7.7812926164057377e+00 2.4973630791939097e+00
15 1.8398608400295208e-01 5.9059792700196434e+00 -9.9161720399808750e+00
16 5.8469261701364097e+00 -2.2571985010582432e+00 2.9857327422767823e+00
17 2.7560211432940238e+00 4.9207971970570350e+00 2.9070576476805532e+00
18 -1.4813870095597501e+00 -1.7378482556644488e+00 -1.6058192501275290e+00
19 1.4804205290003427e+00 -1.2245161773643600e+01 4.9726493930925530e-01
20 -3.6615637886242993e+00 -4.8732204205525411e+00 5.2596344008240576e+00
21 -1.3508123203296574e+00 1.0609703405450992e+01 2.7016894640855278e+00
22 -3.5308456248307213e-01 -1.2267881896396968e+01 3.8041687814180614e-01
23 2.1268575998905277e+00 -9.8195553504983524e-01 -5.0711605404266065e+00
24 6.0440647757301482e+00 -3.8588578230300516e+00 7.2719736140423983e+00
25 8.4455109296650068e+00 7.0624962219255796e+00 -3.1806612774968732e+00
26 -3.0905548748191465e+00 -7.7229205387362132e-01 5.3313905785014661e+00
27 -2.9657410879726704e+00 -8.6651631017774271e+00 -6.7853125584804292e+00
28 4.9373045778342588e+00 6.6292206752376668e+00 4.6463544925063864e+00
29 -6.7596568116029587e+00 1.1854971416292608e+01 -3.1889511538178256e-01
30 -3.1599376372205530e+00 1.2411259590817497e+01 -3.3705452712364457e+00
31 -4.7553805255326909e+00 2.0807423151380857e+00 9.7968713347921295e+00
32 4.7774045900242150e+00 -3.5862707137302143e+00 -3.6201646908067486e+00
1 3.8702196239124556e+00 3.2087381358565223e+00 -3.2785146725167640e+00
2 1.5399659055501953e+00 5.3765327929110578e+00 1.5740005508931318e+00
3 9.6731722224682848e-01 -1.3144867798433951e+01 -9.0231732944275522e-01
4 -2.5073370343026689e+00 -5.2079180074531992e+00 -5.8913203171676738e+00
5 -2.8515169765268102e+00 7.6648779774003026e+00 -1.6135262802375598e+00
6 2.0428463056677881e-01 5.1885731021366395e+00 -5.9322347514395024e-01
7 -9.7176119399521776e-01 3.5285494740740844e+00 3.2284411698902957e+00
8 7.5364432092290057e-01 -5.2936287201395666e+00 -6.2408220629964086e+00
9 -5.8493861425956810e+00 -3.7463543270547230e+00 -3.9409131835957951e+00
10 -1.8023712766218374e+00 3.7006913245202173e+00 -3.8897352514946566e+00
11 3.5323555367961745e-01 -1.1327469434419125e+01 6.7182457803169395e+00
12 -4.4655507115630835e+00 -4.1270694194868245e+00 4.6918435871986608e+00
13 4.4725135751255225e+00 -3.8312677334793439e+00 -2.6917694312022555e-01
14 -2.7336352778319069e+00 7.7812926164057457e+00 2.4973630791940713e+00
15 1.8398608400308647e-01 5.9059792700197038e+00 -9.9161720399810651e+00
16 5.8469261701361397e+00 -2.2571985010583182e+00 2.9857327422767290e+00
17 2.7560211432941584e+00 4.9207971970570217e+00 2.9070576476804888e+00
18 -1.4813870095596227e+00 -1.7378482556645491e+00 -1.6058192501277275e+00
19 1.4804205290004067e+00 -1.2245161773643698e+01 4.9726493930928467e-01
20 -3.6615637886244712e+00 -4.8732204205525784e+00 5.2596344008243827e+00
21 -1.3508123203299385e+00 1.0609703405450899e+01 2.7016894640854958e+00
22 -3.5308456248317949e-01 -1.2267881896396879e+01 3.8041687814183101e-01
23 2.1268575998906152e+00 -9.8195553504959066e-01 -5.0711605404262796e+00
24 6.0440647757302921e+00 -3.8588578230301529e+00 7.2719736140424249e+00
25 8.4455109296649944e+00 7.0624962219256604e+00 -3.1806612774971015e+00
26 -3.0905548748190270e+00 -7.7229205387351962e-01 5.3313905785011455e+00
27 -2.9657410879726527e+00 -8.6651631017773774e+00 -6.7853125584803529e+00
28 4.9373045778342091e+00 6.6292206752377218e+00 4.6463544925066387e+00
29 -6.7596568116029836e+00 1.1854971416292619e+01 -3.1889511538200521e-01
30 -3.1599376372206285e+00 1.2411259590817284e+01 -3.3705452712365678e+00
31 -4.7553805255326385e+00 2.0807423151379889e+00 9.7968713347922520e+00
32 4.7774045900241520e+00 -3.5862707137300642e+00 -3.6201646908068756e+00
run_vdwl: -373.391968845895
run_coul: 0
run_stress: ! |-
-3.9486584521928387e+02 -4.6496789731502832e+02 -4.1710147439166667e+02 1.8213412417226081e+01 7.6724894655338038e-01 1.2094096020348012e+01
-3.9486584521928921e+02 -4.6496789731503287e+02 -4.1710147439167230e+02 1.8213412417225918e+01 7.6724894655356990e-01 1.2094096020347751e+01
run_forces: ! |2
1 3.6065103849698468e+00 3.3850045614133313e+00 -3.2099404138931509e+00
2 1.5272319527263032e+00 5.1159618338839312e+00 1.4386822600144664e+00
3 8.8889124738965819e-01 -1.2549265126891074e+01 -7.6286300397645501e-01
4 -2.5149887025851170e+00 -5.1630477798481431e+00 -5.7927560583461730e+00
5 -2.7577319227243340e+00 7.7337372091606680e+00 -1.6161053768722711e+00
6 2.9829137219780122e-01 4.9518159754562241e+00 -6.3319133869634869e-01
7 -8.7309179105028933e-01 3.7242971801706921e+00 3.1667500872407377e+00
8 7.4988511941705449e-01 -5.2345536588071093e+00 -6.0694489025295839e+00
9 -5.6748652076461674e+00 -3.6155005353015062e+00 -3.8960205269343655e+00
10 -1.6985487726687425e+00 3.3586465595352220e+00 -3.9313302972889002e+00
11 3.0645290480830667e-01 -1.1180223984570517e+01 6.5832137421124841e+00
12 -4.4891921700259347e+00 -4.1479969157235592e+00 4.6314455848790201e+00
13 4.3217028924633345e+00 -3.6856204342214225e+00 -3.0397864454481671e-01
14 -2.5849914165064707e+00 7.5606403552491512e+00 2.3174690493053731e+00
15 1.1796272962339260e-01 5.7288100295841362e+00 -9.7607016326972875e+00
16 5.7880766878601184e+00 -2.4198072924490344e+00 3.0510124864170507e+00
17 2.6948634470285198e+00 4.9491285704784493e+00 2.8470505948516216e+00
18 -1.3885896269097586e+00 -1.7319937370042313e+00 -1.4698594584039826e+00
19 1.3993184597149559e+00 -1.1797240539240345e+01 4.4955145029402199e-01
20 -3.6118153030811628e+00 -4.8252169436385737e+00 5.1301467326003083e+00
21 -1.3245618504864409e+00 1.0413638773882035e+01 2.6136063969881485e+00
22 -3.6531531607881618e-01 -1.2221686471408907e+01 3.4297492050272915e-01
23 2.1591154306811964e+00 -8.2020156536698485e-01 -4.8505116467228593e+00
24 5.8317944566991562e+00 -3.8285931693697965e+00 7.1438153964941415e+00
25 8.3117675961796262e+00 7.0110643410721547e+00 -3.1321086296777607e+00
26 -2.9593072762047514e+00 -7.3717349777411822e-01 5.3317823136164311e+00
27 -2.8851089719214054e+00 -8.5425149524249182e+00 -6.6688154620289835e+00
28 4.7313345552457529e+00 6.4894520960745865e+00 4.4358188230989617e+00
29 -6.6981970679986764e+00 1.1511660045027716e+01 -2.4612864290481729e-01
30 -2.9580050013088863e+00 1.2189750141569847e+01 -3.2455167441500565e+00
31 -4.5434783129378946e+00 1.9394948274115587e+00 9.6218495408600599e+00
32 4.5945894731298162e+00 -3.5624658959294715e+00 -3.5158925996077341e+00
1 3.6065103849699045e+00 3.3850045614132207e+00 -3.2099404138932623e+00
2 1.5272319527262948e+00 5.1159618338837785e+00 1.4386822600145812e+00
3 8.8889124738980918e-01 -1.2549265126891047e+01 -7.6286300397668594e-01
4 -2.5149887025850397e+00 -5.1630477798480570e+00 -5.7927560583462672e+00
5 -2.7577319227244645e+00 7.7337372091604548e+00 -1.6161053768723057e+00
6 2.9829137219776214e-01 4.9518159754561530e+00 -6.3319133869644395e-01
7 -8.7309179105045454e-01 3.7242971801707845e+00 3.1667500872406640e+00
8 7.4988511941697533e-01 -5.2345536588071431e+00 -6.0694489025296816e+00
9 -5.6748652076462358e+00 -3.6155005353015071e+00 -3.8960205269341404e+00
10 -1.6985487726686137e+00 3.3586465595355084e+00 -3.9313302972887927e+00
11 3.0645290480838572e-01 -1.1180223984570464e+01 6.5832137421123793e+00
12 -4.4891921700259259e+00 -4.1479969157236125e+00 4.6314455848788976e+00
13 4.3217028924633798e+00 -3.6856204342215526e+00 -3.0397864454471007e-01
14 -2.5849914165064791e+00 7.5606403552492631e+00 2.3174690493052812e+00
15 1.1796272962344825e-01 5.7288100295841273e+00 -9.7607016326974527e+00
16 5.7880766878599035e+00 -2.4198072924487954e+00 3.0510124864169175e+00
17 2.6948634470284509e+00 4.9491285704784609e+00 2.8470505948517495e+00
18 -1.3885896269096671e+00 -1.7319937370044067e+00 -1.4698594584041307e+00
19 1.3993184597150856e+00 -1.1797240539240288e+01 4.4955145029417165e-01
20 -3.6118153030813107e+00 -4.8252169436387415e+00 5.1301467326004531e+00
21 -1.3245618504865346e+00 1.0413638773882186e+01 2.6136063969881778e+00
22 -3.6531531607884909e-01 -1.2221686471408978e+01 3.4297492050278428e-01
23 2.1591154306812275e+00 -8.2020156536692501e-01 -4.8505116467226950e+00
24 5.8317944566992397e+00 -3.8285931693700967e+00 7.1438153964941540e+00
25 8.3117675961795374e+00 7.0110643410720712e+00 -3.1321086296778664e+00
26 -2.9593072762046271e+00 -7.3717349777414354e-01 5.3317823136164080e+00
27 -2.8851089719213050e+00 -8.5425149524249200e+00 -6.6688154620289044e+00
28 4.7313345552455530e+00 6.4894520960747961e+00 4.4358188230991802e+00
29 -6.6981970679986054e+00 1.1511660045027632e+01 -2.4612864290500908e-01
30 -2.9580050013088357e+00 1.2189750141569929e+01 -3.2455167441500277e+00
31 -4.5434783129378431e+00 1.9394948274115187e+00 9.6218495408601559e+00
32 4.5945894731298269e+00 -3.5624658959292090e+00 -3.5158925996075792e+00
...

7
unittest/force-styles/tests/atomic-pair-eam_alloy.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Fri May 15 23:19:20 202
epsilon: 5.0e-12
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-12
prerequisites: ! |
pair eam/alloy
pre_commands: ! ""
@ -10,6 +10,7 @@ input_file: in.metal
pair_style: eam/alloy
pair_coeff: ! |
* * CuNi.eam.alloy Cu Ni
extract: ! ""
natoms: 32
init_vdwl: -118.717513292074
init_coul: 0

138
unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 11:40:47 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 7.5e-12
prerequisites: ! |
pair eam/alloy
@ -13,78 +13,78 @@ pair_coeff: ! |
* * CuNi.eam.alloy Cu Ni
extract: ! ""
natoms: 32
init_vdwl: -2737.69103243003
init_vdwl: -2737.69103243002
init_coul: 0
init_stress: ! |2-
1.1764167914492630e+03 1.1205980824873152e+03 1.0864455580994877e+03 8.1647231129875934e+01 -2.5037139879631205e+01 -6.3600641311729632e+01
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init_forces: ! |2
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2 -1.0636773406463684e+01 -4.4073764067943728e+01 2.0771028937481248e+01
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21 8.5316643556023976e+01 1.4311382265670481e+01 1.3218228731927237e+00
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28 -4.7832347888399553e+00 2.6723575502863451e+01 3.5294244672039667e+01
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32 -1.0162711573460497e+02 -2.1279270671809819e+01 -6.5117201231272759e+00
run_vdwl: 13786.8231164129
run_coul: 0
run_stress: ! |2-
1.5453045758769309e+04 1.4324564159674526e+04 2.0339719265203345e+04 -4.3703985097767185e+02 -2.4828700331963573e+03 2.6371860977250676e+03
1.5453045758769322e+04 1.4324564159674677e+04 2.0339719265203443e+04 -4.3703985097767946e+02 -2.4828700331963387e+03 2.6371860977250767e+03
run_forces: ! |2
1 -4.1235070358044659e+03 -1.6712537087260623e+02 1.0285277274671844e+02
2 -1.7134569288200260e+03 5.6109874495911663e+02 1.5833880163322256e+03
3 7.0660491674313107e+02 1.9980947258587582e+02 3.5478310177110990e+02
4 -1.5805950092619389e+02 -6.3394860464940950e+02 -8.2522020103607213e+02
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6 4.1907332132232949e+02 4.0962894944175537e+02 1.0986647025780044e+03
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8 1.0265438581270025e+03 2.0808489842263230e+03 2.0164534268299593e+02
9 1.1337966507234397e+02 -5.0396233184209956e+02 3.8179698908837855e+02
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26 1.0172211816330166e+03 -9.5258495026630271e+02 -3.7013789400208348e+03
27 -9.3684148116058168e+02 4.9006556088962077e+02 4.5089073710681362e+02
28 2.6547988549156607e+03 5.0325157403920798e+02 5.1846329264498172e+03
29 1.3361686744155759e+03 2.5910193783558044e-01 1.0501345350932138e+03
30 4.1083282961451374e+02 6.3716214702024570e+02 -3.1059177937091081e+03
31 2.2436377537176998e+02 -5.0079917535823370e+02 6.8158392999295666e+02
32 -2.4717482535028950e+02 -1.4570181605226253e+02 -2.8412607206596545e+02
...

120
unittest/force-styles/tests/atomic-pair-eam_cd.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Tue May 26 20:03:05 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-12
prerequisites: ! |
pair eam/cd
@ -18,73 +18,73 @@ init_coul: 0
init_stress: ! |2-
2.9506366554526057e+01 2.9183156291462467e+01 2.2317338076293908e+01 7.8583791220531909e+00 -9.3405164902515037e-01 8.4666514895851674e-01
init_forces: ! |2
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11 -7.8479707378783470e-01 -6.2993144003952650e-01 6.3942912806742538e-02
13 5.1991737344816569e-01 6.7753655352037012e-01 -4.2253607965493278e-01
18 -3.9298044850749392e+00 -1.5616705686457237e+00 -1.9169690454319406e+00
29 1.4880693724627443e+00 3.4962901394738459e+00 -3.6870129713529731e-01
4 4.2543046025430409e-01 -9.7237717899675247e-01 -9.7112607187150968e-01
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22 -2.8479665623063127e-01 -2.0662756239881088e+00 8.5531412410115235e-02
25 2.5703560958845761e+00 1.5017045624035867e+00 -1.2891287546837082e-01
3 -9.4232987410053415e-01 1.1082132149610051e+00 -6.0528613124462960e-01
10 -2.8152383871264947e-01 -1.1137434307914110e-01 -7.1867606993919331e-01
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32 -2.6135587355983043e+00 -1.5330500443455732e+00 -6.7557011932914857e-01
run_vdwl: -77.65496555698
run_coul: 0
run_stress: ! |2-
2.8585743222299783e+01 2.8300763599883620e+01 2.1800410375921810e+01 7.4500400291680950e+00 -1.0636039604288940e+00 8.4740666819864296e-01
run_forces: ! |2
8 -2.7151053004591208e-01 -1.5287399675025755e+00 -5.4534089864381885e-01
11 -7.6679766845686814e-01 -6.3322365651311130e-01 4.7728049772552503e-02
13 5.0939531182086928e-01 6.8413494991310242e-01 -4.2098815476105311e-01
18 -3.6892936686513820e+00 -1.4556828938869788e+00 -1.8103278324839420e+00
29 1.3407876110200074e+00 3.3111406589372017e+00 -3.3732975630652123e-01
4 4.0807816914053147e-01 -9.4566550283660311e-01 -9.5348608946481239e-01
9 -4.1823699825935307e-01 -3.0754071802614963e-01 -1.1183696132595670e-01
15 -7.2508155408548902e-01 1.5144677531296626e+00 -1.0864955300224399e+00
22 -2.2054525313872317e-01 -1.9984312218234146e+00 7.1900794989121525e-02
25 2.4910528464915269e+00 1.4658890698067975e+00 -1.3869148162687062e-01
3 -9.4063283702315814e-01 1.0775755551349597e+00 -5.9775647301115542e-01
10 -2.5002184738752448e-01 -1.0198477234944650e-01 -6.6684588027858072e-01
16 2.2898405388879040e+00 -1.1378953314614961e+00 -8.4272711131861044e-01
21 1.4790878931837190e+00 1.7136887929621036e+00 1.1269633038157936e+00
26 -1.4106451720861932e+00 -1.5618537601149505e+00 9.7574227521752288e-01
7 -1.0741108869644040e+00 1.2831430885766124e+00 -5.4667017037232546e-01
12 1.5816856488010231e+00 -9.1902882640923744e-01 -5.6535909175480059e-01
17 4.7161383076462332e-01 1.9565174525684229e-01 9.3819195032752134e-01
30 -4.5762456300468696e-01 6.6407205464735841e-01 -6.9428727830465098e-01
2 -8.5490517434075847e-02 -2.1659172685616215e-01 5.0142370520318835e-01
19 -2.3085159711941969e+00 -2.9612141261464395e+00 3.7188702337674601e-01
24 4.2941840668820070e+00 1.9468832898802828e+00 2.2380972699887196e+00
27 2.0890840531702448e-01 3.5786474239715432e-01 6.2130307644364287e-02
6 -5.5245666180980457e-01 6.4138882034278044e-01 -4.8007835354561723e-01
20 5.3179718158105560e-01 -4.7602396117212981e-01 3.0623145836571120e-01
31 -8.1236514734795273e-01 -1.3407493053805772e+00 2.3754011704155875e+00
5 -7.2493198432645400e-01 5.4807444983935638e-01 4.8889246609771136e-01
28 -3.7176754911744125e-01 2.5654240520686689e-01 1.3306741973778954e-01
32 -2.5983287754819857e+00 -1.4915067587850344e+00 -6.6646013114343972e-01
1 3.4169448683529990e-01 -3.1004791972686529e-02 -2.4769580345365880e-01
2 -8.5490517434075847e-02 -2.1659172685616215e-01 5.0142370520318835e-01
3 -9.4063283702315814e-01 1.0775755551349597e+00 -5.9775647301115542e-01
4 4.0807816914053147e-01 -9.4566550283660311e-01 -9.5348608946481239e-01
5 -7.2493198432645400e-01 5.4807444983935638e-01 4.8889246609771136e-01
6 -5.5245666180980457e-01 6.4138882034278044e-01 -4.8007835354561723e-01
7 -1.0741108869644040e+00 1.2831430885766124e+00 -5.4667017037232546e-01
8 -2.7151053004591208e-01 -1.5287399675025755e+00 -5.4534089864381885e-01
9 -4.1823699825935307e-01 -3.0754071802614963e-01 -1.1183696132595670e-01
10 -2.5002184738752448e-01 -1.0198477234944650e-01 -6.6684588027858072e-01
11 -7.6679766845686814e-01 -6.3322365651311130e-01 4.7728049772552503e-02
12 1.5816856488010231e+00 -9.1902882640923744e-01 -5.6535909175480059e-01
13 5.0939531182086928e-01 6.8413494991310242e-01 -4.2098815476105311e-01
14 5.0573882893138455e-01 -3.8622187936633440e-01 1.3985322998607304e+00
15 -7.2508155408548902e-01 1.5144677531296626e+00 -1.0864955300224399e+00
16 2.2898405388879040e+00 -1.1378953314614961e+00 -8.4272711131861044e-01
17 4.7161383076462332e-01 1.9565174525684229e-01 9.3819195032752134e-01
18 -3.6892936686513820e+00 -1.4556828938869788e+00 -1.8103278324839420e+00
19 -2.3085159711941969e+00 -2.9612141261464395e+00 3.7188702337674601e-01
20 5.3179718158105560e-01 -4.7602396117212981e-01 3.0623145836571120e-01
21 1.4790878931837190e+00 1.7136887929621036e+00 1.1269633038157936e+00
22 -2.2054525313872317e-01 -1.9984312218234146e+00 7.1900794989121525e-02
23 1.2244927661586273e+00 1.8328418245722449e+00 -3.2381249699480508e-01
24 4.2941840668820070e+00 1.9468832898802828e+00 2.2380972699887196e+00
25 2.4910528464915269e+00 1.4658890698067975e+00 -1.3869148162687062e-01
26 -1.4106451720861932e+00 -1.5618537601149505e+00 9.7574227521752288e-01
27 2.0890840531702448e-01 3.5786474239715432e-01 6.2130307644364287e-02
28 -3.7176754911744125e-01 2.5654240520686689e-01 1.3306741973778954e-01
29 1.3407876110200074e+00 3.3111406589372017e+00 -3.3732975630652123e-01
30 -4.5762456300468696e-01 6.6407205464735841e-01 -6.9428727830465098e-01
31 -8.1236514734795273e-01 -1.3407493053805772e+00 2.3754011704155875e+00
32 -2.5983287754819857e+00 -1.4915067587850344e+00 -6.6646013114343972e-01
...

120
unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 5 May 2020
date_generated: Thu May 28 06:23:01 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-12
prerequisites: ! |
pair eam/cd/old
@ -18,73 +18,73 @@ init_coul: 0
init_stress: ! |2-
2.9405509133096274e+01 2.9077568336065784e+01 2.2113739361139935e+01 7.8904933627522267e+00 -9.3663625990408816e-01 8.1130320719355153e-01
init_forces: ! |2
8 -2.4395655011794004e-01 -1.5333218084741596e+00 -5.5245484545491697e-01
11 -7.8706069939087697e-01 -6.3256079782490671e-01 5.4125643283892681e-02
13 5.1518155226706963e-01 6.8274677994766197e-01 -4.2850986846545980e-01
18 -3.9256582801572564e+00 -1.5618588551742114e+00 -1.9139821131009855e+00
29 1.4999378064208269e+00 3.4792718713414832e+00 -3.6648974322266664e-01
4 4.2464232689549453e-01 -9.7164204677538535e-01 -9.7219077261848585e-01
9 -4.1883835783416828e-01 -2.9640623407730660e-01 -9.3659089760684641e-02
15 -7.7638636434137465e-01 1.5329378947070542e+00 -1.1035208637789840e+00
22 -2.8700086895519467e-01 -2.0643765194685284e+00 8.5229634089584366e-02
25 2.5743829864820831e+00 1.5066523137107746e+00 -1.2624906599123387e-01
3 -9.0726681299683187e-01 1.0619426753822845e+00 -5.8362819906686325e-01
10 -2.7746664677947930e-01 -9.9414875982860917e-02 -6.9345163681304967e-01
16 2.3481539742343385e+00 -1.1310953819765714e+00 -8.5356283146096967e-01
21 1.5363256394734701e+00 1.8113878750853332e+00 1.1372797726733304e+00
26 -1.5263877243918971e+00 -1.6426898707601700e+00 1.0185360426954311e+00
7 -1.0984506174307791e+00 1.2895286552767053e+00 -5.4447897480978547e-01
12 1.6057913185256654e+00 -9.4698230673325845e-01 -5.8571244556639712e-01
17 4.6309553650227248e-01 1.9577141871283613e-01 9.4588389196297584e-01
30 -4.8103274177570204e-01 6.7765823339012321e-01 -7.2776907743413610e-01
2 -9.6746966328518896e-02 -2.0660058647238458e-01 5.1376678118360786e-01
19 -2.4660378601709181e+00 -3.1428997639171015e+00 3.6929505266594292e-01
24 4.6125255774631988e+00 2.0934708458658551e+00 2.3354130173781136e+00
27 1.6537006967519022e-01 4.0030582114974539e-01 7.6202897807556333e-02
6 -5.5673454781795384e-01 6.4352466176927337e-01 -5.0416324732898266e-01
20 5.3753132262499415e-01 -4.8016263425435718e-01 3.2102890572308612e-01
31 -8.5335875768564051e-01 -1.3518208677019026e+00 2.4663641279666662e+00
5 -7.4639221870381012e-01 5.6748273743689703e-01 5.0398965766459269e-01
28 -3.3427836201448913e-01 2.2430792656431101e-01 1.1564659047727996e-01
32 -2.6142628689137353e+00 -1.5189868845729886e+00 -6.7390297673000232e-01
1 3.7750702521380647e-01 -1.2775122604877289e-02 -2.3192012230744505e-01
2 -9.6746966328518896e-02 -2.0660058647238458e-01 5.1376678118360786e-01
3 -9.0726681299683187e-01 1.0619426753822845e+00 -5.8362819906686325e-01
4 4.2464232689549453e-01 -9.7164204677538535e-01 -9.7219077261848585e-01
5 -7.4639221870381012e-01 5.6748273743689703e-01 5.0398965766459269e-01
6 -5.5673454781795384e-01 6.4352466176927337e-01 -5.0416324732898266e-01
7 -1.0984506174307791e+00 1.2895286552767053e+00 -5.4447897480978547e-01
8 -2.4395655011794004e-01 -1.5333218084741596e+00 -5.5245484545491697e-01
9 -4.1883835783416828e-01 -2.9640623407730660e-01 -9.3659089760684641e-02
10 -2.7746664677947930e-01 -9.9414875982860917e-02 -6.9345163681304967e-01
11 -7.8706069939087697e-01 -6.3256079782490671e-01 5.4125643283892681e-02
12 1.6057913185256654e+00 -9.4698230673325845e-01 -5.8571244556639712e-01
13 5.1518155226706963e-01 6.8274677994766197e-01 -4.2850986846545980e-01
14 4.9905260884493080e-01 -4.3548863736972288e-01 1.3704420563876023e+00
15 -7.7638636434137465e-01 1.5329378947070542e+00 -1.1035208637789840e+00
16 2.3481539742343385e+00 -1.1310953819765714e+00 -8.5356283146096967e-01
17 4.6309553650227248e-01 1.9577141871283613e-01 9.4588389196297584e-01
18 -3.9256582801572564e+00 -1.5618588551742114e+00 -1.9139821131009855e+00
19 -2.4660378601709181e+00 -3.1428997639171015e+00 3.6929505266594292e-01
20 5.3753132262499415e-01 -4.8016263425435718e-01 3.2102890572308612e-01
21 1.5363256394734701e+00 1.8113878750853332e+00 1.1372797726733304e+00
22 -2.8700086895519467e-01 -2.0643765194685284e+00 8.5229634089584366e-02
23 1.2378195011832249e+00 1.8620934838003551e+00 -3.5755819804861416e-01
24 4.6125255774631988e+00 2.0934708458658551e+00 2.3354130173781136e+00
25 2.5743829864820831e+00 1.5066523137107746e+00 -1.2624906599123387e-01
26 -1.5263877243918971e+00 -1.6426898707601700e+00 1.0185360426954311e+00
27 1.6537006967519022e-01 4.0030582114974539e-01 7.6202897807556333e-02
28 -3.3427836201448913e-01 2.2430792656431101e-01 1.1564659047727996e-01
29 1.4999378064208269e+00 3.4792718713414832e+00 -3.6648974322266664e-01
30 -4.8103274177570204e-01 6.7765823339012321e-01 -7.2776907743413610e-01
31 -8.5335875768564051e-01 -1.3518208677019026e+00 2.4663641279666662e+00
32 -2.6142628689137353e+00 -1.5189868845729886e+00 -6.7390297673000232e-01
run_vdwl: -77.5908146669562
run_coul: 0
run_stress: ! |2-
2.8485191578893058e+01 2.8198695634641155e+01 2.1600480977108983e+01 7.4831961344053015e+00 -1.0657036014691093e+00 8.1083296213634959e-01
run_forces: ! |2
8 -2.6687662328951439e-01 -1.5323983128806480e+00 -5.3650003340444363e-01
11 -7.6894416406912669e-01 -6.3558503412677736e-01 3.8197957557271150e-02
13 5.0470405196269419e-01 6.8947168162484451e-01 -4.2691120946149397e-01
18 -3.6854522670425158e+00 -1.4559988082140753e+00 -1.8074005610504837e+00
29 1.3524738452403593e+00 3.2946498298818288e+00 -3.3499173170850133e-01
4 4.0729758180114273e-01 -9.4491662268062182e-01 -9.5450134374689677e-01
9 -4.1599974909284382e-01 -3.0446259231679634e-01 -1.1153295601432243e-01
15 -7.2971570976124900e-01 1.5042763436302977e+00 -1.0747802112135652e+00
22 -2.2250198294686541e-01 -1.9965841181629400e+00 7.1747050733221227e-02
25 2.4950084662696983e+00 1.4707797579395552e+00 -1.3594695871930362e-01
3 -9.0534014592010392e-01 1.0332760987936294e+00 -5.7650969402625052e-01
10 -2.4598170004171149e-01 -9.1061063106574108e-02 -6.4286211566594620e-01
16 2.2585093380006076e+00 -1.1168061549089283e+00 -8.4057202310250323e-01
21 1.4601582272558056e+00 1.7066533856947079e+00 1.1129911037189397e+00
26 -1.4181737451422176e+00 -1.5291168458460618e+00 9.5602794273735947e-01
7 -1.0726809843117340e+00 1.2799606830754382e+00 -5.4314026901401546e-01
12 1.5850988167998827e+00 -9.1572194416915975e-01 -5.6882585734207169e-01
17 4.7006057082843539e-01 1.9337850521959463e-01 9.3772077301591306e-01
30 -4.5467752591799759e-01 6.6316947806197213e-01 -6.9376708110580343e-01
2 -8.8659229971455075e-02 -2.1347769705954714e-01 5.0057777700323369e-01
19 -2.3079714228833410e+00 -2.9608093698018987e+00 3.7108228042443869e-01
24 4.2950019630782688e+00 1.9475688188592346e+00 2.2351682655037335e+00
27 1.7749931668796490e-01 3.8675424964670363e-01 5.9748810010048489e-02
6 -5.4727635910881256e-01 6.3807859667675315e-01 -4.7985870047603307e-01
20 5.2623598439294483e-01 -4.7516744794791216e-01 3.0914307217963943e-01
31 -8.0935941564949265e-01 -1.3301958218136074e+00 2.3859777045237114e+00
5 -7.2603632278983410e-01 5.5101408460680934e-01 4.8498734148834588e-01
28 -3.4089135725955205e-01 2.2341523534112284e-01 1.2257324449666285e-01
32 -2.5991916652162788e+00 -1.4776784092373672e+00 -6.6499163713851406e-01
1 3.4051925606376454e-01 -2.6258862226114895e-02 -2.5087755767694686e-01
2 -8.8659229971455075e-02 -2.1347769705954714e-01 5.0057777700323369e-01
3 -9.0534014592010392e-01 1.0332760987936294e+00 -5.7650969402625052e-01
4 4.0729758180114273e-01 -9.4491662268062182e-01 -9.5450134374689677e-01
5 -7.2603632278983410e-01 5.5101408460680934e-01 4.8498734148834588e-01
6 -5.4727635910881256e-01 6.3807859667675315e-01 -4.7985870047603307e-01
7 -1.0726809843117340e+00 1.2799606830754382e+00 -5.4314026901401546e-01
8 -2.6687662328951439e-01 -1.5323983128806480e+00 -5.3650003340444363e-01
9 -4.1599974909284382e-01 -3.0446259231679634e-01 -1.1153295601432243e-01
10 -2.4598170004171149e-01 -9.1061063106574108e-02 -6.4286211566594620e-01
11 -7.6894416406912669e-01 -6.3558503412677736e-01 3.8197957557271150e-02
12 1.5850988167998827e+00 -9.1572194416915975e-01 -5.6882585734207169e-01
13 5.0470405196269419e-01 6.8947168162484451e-01 -4.2691120946149397e-01
14 5.0915603335540283e-01 -4.0999165632064422e-01 1.3825486730786496e+00
15 -7.2971570976124900e-01 1.5042763436302977e+00 -1.0747802112135652e+00
16 2.2585093380006076e+00 -1.1168061549089283e+00 -8.4057202310250323e-01
17 4.7006057082843539e-01 1.9337850521959463e-01 9.3772077301591306e-01
18 -3.6854522670425158e+00 -1.4559988082140753e+00 -1.8074005610504837e+00
19 -2.3079714228833410e+00 -2.9608093698018987e+00 3.7108228042443869e-01
20 5.2623598439294483e-01 -4.7516744794791216e-01 3.0914307217963943e-01
21 1.4601582272558056e+00 1.7066533856947079e+00 1.1129911037189397e+00
22 -2.2250198294686541e-01 -1.9965841181629400e+00 7.1747050733221227e-02
23 1.2240069186776739e+00 1.8337840117671826e+00 -3.2452205560407349e-01
24 4.2950019630782688e+00 1.9475688188592346e+00 2.2351682655037335e+00
25 2.4950084662696983e+00 1.4707797579395552e+00 -1.3594695871930362e-01
26 -1.4181737451422176e+00 -1.5291168458460618e+00 9.5602794273735947e-01
27 1.7749931668796490e-01 3.8675424964670363e-01 5.9748810010048489e-02
28 -3.4089135725955205e-01 2.2341523534112284e-01 1.2257324449666285e-01
29 1.3524738452403593e+00 3.2946498298818288e+00 -3.3499173170850133e-01
30 -4.5467752591799759e-01 6.6316947806197213e-01 -6.9376708110580343e-01
31 -8.0935941564949265e-01 -1.3301958218136074e+00 2.3859777045237114e+00
32 -2.5991916652162788e+00 -1.4776784092373672e+00 -6.6499163713851406e-01
...

130
unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 15:30:51 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-12
prerequisites: ! |
pair eam/cd
@ -17,75 +17,75 @@ natoms: 32
init_vdwl: -1785.33573859861
init_coul: 0
init_stress: ! |2-
6.8043301174259739e+02 6.7297960563391212e+02 5.1465006825793432e+02 1.8121853680469485e+02 -2.1539743820861840e+01 1.9524563154151586e+01
6.8043301174259761e+02 6.7297960563391200e+02 5.1465006825793444e+02 1.8121853680469479e+02 -2.1539743820861666e+01 1.9524563154151824e+01
init_forces: ! |2
8 -5.7350284149741624e+00 -3.5278567560873412e+01 -1.2945450320411185e+01
11 -1.8097851375135637e+01 -1.4526564839671716e+01 1.4745586739847019e+00
13 1.1989580066351607e+01 1.5624364891748142e+01 -9.7439139691488030e+00
18 -9.0623448888489833e+01 -3.6012980670109037e+01 -4.4206358603667979e+01
29 3.4315696679075806e+01 8.0626370079554022e+01 -8.5024543289523695e+00
4 9.8106599747837144e+00 -2.2423551582732831e+01 -2.2394700365566653e+01
9 -9.7103731975151177e+00 -6.9064607099453728e+00 -2.1661283927312738e+00
15 -1.7792920650091148e+01 3.5590552950398063e+01 -2.5723318396810825e+01
22 -6.5675672460417749e+00 -4.7649450274482049e+01 1.9724013269199872e+00
25 5.9273822696594358e+01 3.4630131644829056e+01 -2.9728016814706639e+00
3 -2.1730644235860989e+01 2.5556005146056687e+01 -1.3958230488587832e+01
10 -6.4920942773028782e+00 -2.5683534959198733e+00 -1.6573064725963313e+01
16 5.4866106162193525e+01 -2.6559412741299443e+01 -1.9741676495697597e+01
21 3.5877005997488176e+01 4.1948795376449915e+01 2.6549358660124593e+01
26 -3.5041054144373000e+01 -3.8690624501424864e+01 2.3990991622029867e+01
7 -2.5368323752589127e+01 2.9810504132177154e+01 -1.2638531317689472e+01
12 3.6951069676944783e+01 -2.1917541992301505e+01 -1.3427277677714791e+01
17 1.0715624362332361e+01 4.5671651640165596e+00 2.1824770610292802e+01
30 -1.1158262405262283e+01 1.5645450981201234e+01 -1.6793195768740460e+01
2 -2.1575934430928174e+00 -4.8375617933428616e+00 1.1868004064201370e+01
1 8.7363936089779699e+00 -4.0061891709735753e-01 -5.2750678284773107e+00
2 -2.1575934430928165e+00 -4.8375617933428607e+00 1.1868004064201370e+01
3 -2.1730644235860975e+01 2.5556005146056709e+01 -1.3958230488587796e+01
4 9.8106599747837162e+00 -2.2423551582732884e+01 -2.2394700365566706e+01
5 -1.7188199887458431e+01 1.3020595354001870e+01 1.1713947051593557e+01
6 -1.2960045695799428e+01 1.4917602053253173e+01 -1.1634623653327418e+01
7 -2.5368323752589124e+01 2.9810504132177154e+01 -1.2638531317689470e+01
8 -5.7350284149741588e+00 -3.5278567560873405e+01 -1.2945450320411185e+01
9 -9.7103731975151177e+00 -6.9064607099453683e+00 -2.1661283927312853e+00
10 -6.4920942773028836e+00 -2.5683534959199092e+00 -1.6573064725963359e+01
11 -1.8097851375135640e+01 -1.4526564839671718e+01 1.4745586739847021e+00
12 3.6951069676944790e+01 -2.1917541992301501e+01 -1.3427277677714789e+01
13 1.1989580066351609e+01 1.5624364891748140e+01 -9.7439139691488137e+00
14 1.1426402460118316e+01 -9.4966708566757578e+00 3.1977067658213798e+01
15 -1.7792920650091144e+01 3.5590552950398035e+01 -2.5723318396810786e+01
16 5.4866106162193503e+01 -2.6559412741299433e+01 -1.9741676495697597e+01
17 1.0715624362332365e+01 4.5671651640165614e+00 2.1824770610292806e+01
18 -9.0623448888489847e+01 -3.6012980670109037e+01 -4.4206358603667979e+01
19 -5.6881035489195945e+01 -7.2486978424465079e+01 8.5346400279864998e+00
20 1.2523060387800896e+01 -1.1092095621986930e+01 7.3361549932744241e+00
21 3.5877005997488176e+01 4.1948795376449915e+01 2.6549358660124597e+01
22 -6.5675672460417234e+00 -4.7649450274482064e+01 1.9724013269199587e+00
23 2.8557983431932612e+01 4.2922771735639664e+01 -8.2298364085589846e+00
24 1.0635249022606776e+02 4.8261805685832684e+01 5.3930408354403887e+01
27 4.5450128358507476e+00 8.5625984164024569e+00 1.8060331715170475e+00
6 -1.2960045695799433e+01 1.4917602053253173e+01 -1.1634623653327418e+01
20 1.2523060387800900e+01 -1.1092095621986928e+01 7.3361549932744214e+00
31 -1.9746718194509153e+01 -3.1423401701143103e+01 5.6625794900273178e+01
5 -1.7188199887458431e+01 1.3020595354001873e+01 1.1713947051593561e+01
28 -8.4196479821767927e+00 5.9390977389974946e+00 2.9015171484281339e+00
32 -6.0270099286644097e+01 -3.5352975667087023e+01 -1.5579017839726889e+01
1 8.7363936089779717e+00 -4.0061891709735753e-01 -5.2750678284773072e+00
14 1.1426402460118315e+01 -9.4966708566757614e+00 3.1977067658213787e+01
23 2.8557983431932612e+01 4.2922771735639678e+01 -8.2298364085589899e+00
25 5.9273822696594358e+01 3.4630131644829120e+01 -2.9728016814706089e+00
26 -3.5041054144373000e+01 -3.8690624501424864e+01 2.3990991622029867e+01
27 4.5450128358507227e+00 8.5625984164024338e+00 1.8060331715170492e+00
28 -8.4196479821767962e+00 5.9390977389974946e+00 2.9015171484281326e+00
29 3.4315696679075756e+01 8.0626370079554093e+01 -8.5024543289523482e+00
30 -1.1158262405262278e+01 1.5645450981201224e+01 -1.6793195768740453e+01
31 -1.9746718194509157e+01 -3.1423401701143103e+01 5.6625794900273171e+01
32 -6.0270099286644076e+01 -3.5352975667087023e+01 -1.5579017839726909e+01
run_vdwl: 50833.2095623296
run_coul: 0
run_stress: ! |2-
1.1422757276809528e+06 6.4698538309370587e+05 4.1051148563743639e+05 9.5363304679864508e+04 -1.8362039585635712e+05 -1.1661012466179539e+05
1.1422757276809535e+06 6.4698538309370563e+05 4.1051148563743685e+05 9.5363304679863315e+04 -1.8362039585635814e+05 -1.1661012466179531e+05
run_forces: ! |2
8 -7.4661838460394447e+03 -1.1211419092422286e+03 -9.9785680647352237e+03
11 -1.2156739748086065e+03 -2.5965260670035150e+03 1.0931787195989891e+03
13 1.8896681608362815e+00 4.8691607259253615e+00 -1.2350445460364599e+00
18 9.6833281561496918e+01 2.3040573196963848e+02 -5.8045206738908905e+02
29 -1.1522875720670490e+04 2.1859177429597104e+04 6.6026924351739190e+03
4 8.2866585144562814e+03 2.1987889627894292e+03 -7.3269584596262430e+03
9 -4.6751202227701178e+04 -4.5455389599126109e+04 6.9310666457731364e+04
15 -1.7479956445491218e+03 -1.6324715355756180e+03 -3.8088738011660148e+03
22 5.9705595976766408e+05 -7.3498559170154767e+04 -2.8830207944910129e+05
25 -6.2964336519821500e+05 1.0487031227925362e+06 -4.2163928496550000e+05
3 -3.9919676312365680e+05 -2.9469092131577781e+05 4.7182000013219666e+04
10 1.7089467526999904e+03 1.5998419382683467e+03 3.7660701226776023e+03
16 -6.0049578751180682e+05 6.0547722741760917e+04 2.7117954880042706e+05
21 -6.4190745440347127e+03 -5.4746193210828164e+02 9.9912667127815421e+03
26 -1.2400361710263705e+02 -1.6482646184110337e+02 -1.3181023673232635e+03
7 -4.4527084366605749e+01 1.2083311421562247e+02 1.4090365320304585e+02
12 -9.1471177123676614e+02 8.8769239275791806e+03 2.4590954021189188e+02
17 1.0955176820986494e+06 -7.3097457868150948e+05 3.0732902700087230e+05
30 -8.8479117293965359e+00 3.9144652621120715e+00 -2.5741472917180555e+00
2 -7.6357102464059466e+01 1.1233035238477746e+03 -6.8826275473684859e+02
19 1.7252084357421222e+03 -1.1971214382248461e+03 9.6479329686047180e+01
24 -9.4115440774054568e+03 1.4868082917729369e+04 9.5344712883688553e+03
27 -2.0206241875051235e+03 8.9736344917421525e+02 2.7371544379914644e+02
6 -8.7269440254898427e+00 -4.2871068258170384e+00 -2.8071174977249303e+01
20 1.3147736477952498e+04 4.5528169367928713e+03 1.4550409304372299e+04
31 1.6062724190796675e+02 -3.5009702848199751e+01 1.5780906691469211e+01
1 -6.8825417922686768e+02 -6.9446834170851105e+01 -8.7132365430256675e+02
2 -7.6357102464059423e+01 1.1233035238477735e+03 -6.8826275473684734e+02
3 -3.9919676312365674e+05 -2.9469092131577787e+05 4.7182000013219702e+04
4 8.2866585144562814e+03 2.1987889627894288e+03 -7.3269584596262494e+03
5 4.6327746018426421e+02 -4.2009134275606988e+02 -2.3788165159758432e+03
28 1.2720985720833841e+02 1.6004798320652958e+02 1.3546485540637436e+03
32 -1.5462086679694039e+03 -9.9085693678647149e+03 -6.7979735229861799e+03
1 -6.8825417922686677e+02 -6.9446834170851020e+01 -8.7132365430256550e+02
14 3.2489354130384271e+01 -1.8199012589513091e+00 -1.2103425811994843e+01
23 9.7820842419642543e+02 -3.4289927091667496e+03 1.0679111325906679e+03
6 -8.7269440254898623e+00 -4.2871068258170464e+00 -2.8071174977249292e+01
7 -4.4527084366606331e+01 1.2083311421562198e+02 1.4090365320304448e+02
8 -7.4661838460394392e+03 -1.1211419092422277e+03 -9.9785680647352146e+03
9 -4.6751202227701106e+04 -4.5455389599126021e+04 6.9310666457731480e+04
10 1.7089467526999974e+03 1.5998419382683530e+03 3.7660701226776137e+03
11 -1.2156739748086090e+03 -2.5965260670035136e+03 1.0931787195989884e+03
12 -9.1471177123677103e+02 8.8769239275792152e+03 2.4590954021189071e+02
13 1.8896681608363186e+00 4.8691607259253598e+00 -1.2350445460363511e+00
14 3.2489354130384342e+01 -1.8199012589513384e+00 -1.2103425811994835e+01
15 -1.7479956445491289e+03 -1.6324715355756241e+03 -3.8088738011660262e+03
16 -6.0049578751180659e+05 6.0547722741760830e+04 2.7117954880042735e+05
17 1.0955176820986504e+06 -7.3097457868151064e+05 3.0732902700087085e+05
18 9.6833281561496960e+01 2.3040573196963862e+02 -5.8045206738908939e+02
19 1.7252084357421229e+03 -1.1971214382248465e+03 9.6479329686047492e+01
20 1.3147736477952492e+04 4.5528169367928685e+03 1.4550409304372291e+04
21 -6.4190745440347182e+03 -5.4746193210828221e+02 9.9912667127815548e+03
22 5.9705595976766385e+05 -7.3498559170154767e+04 -2.8830207944910158e+05
23 9.7820842419642599e+02 -3.4289927091667382e+03 1.0679111325906649e+03
24 -9.4115440774054550e+03 1.4868082917729362e+04 9.5344712883688589e+03
25 -6.2964336519821582e+05 1.0487031227925373e+06 -4.2163928496549878e+05
26 -1.2400361710263704e+02 -1.6482646184110337e+02 -1.3181023673232635e+03
27 -2.0206241875051242e+03 8.9736344917421536e+02 2.7371544379914650e+02
28 1.2720985720833842e+02 1.6004798320652955e+02 1.3546485540637434e+03
29 -1.1522875720670545e+04 2.1859177429597163e+04 6.6026924351739308e+03
30 -8.8479117293965324e+00 3.9144652621120195e+00 -2.5741472917180985e+00
31 1.6062724190796649e+02 -3.5009702848199694e+01 1.5780906691469243e+01
32 -1.5462086679694005e+03 -9.9085693678646985e+03 -6.7979735229861662e+03
...

7
unittest/force-styles/tests/atomic-pair-eam_fs.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Fri May 15 23:19:20 202
epsilon: 5.0e-12
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 5e-12
prerequisites: ! |
pair eam/fs
pre_commands: ! ""
@ -10,6 +10,7 @@ input_file: in.metal
pair_style: eam/fs
pair_coeff: ! |
* * AlFe_mm.eam.fs Al Fe
extract: ! ""
natoms: 32
init_vdwl: -108.262111462389
init_coul: 0

138
unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 11:40:47 202
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:21 202
epsilon: 7.5e-12
prerequisites: ! |
pair eam/fs
@ -16,75 +16,75 @@ natoms: 32
init_vdwl: -2496.58372622189
init_coul: 0
init_stress: ! |2-
2.3033019789741047e+03 2.1157417403923514e+03 2.0201355767290902e+03 1.3625967475024967e+02 -4.9118825128592029e+01 8.0062189596557349e+00
2.3033019789742661e+03 2.1157417403924674e+03 2.0201355767292255e+03 1.3625967475023566e+02 -4.9118825128602921e+01 8.0062189596547757e+00
init_forces: ! |2
1 3.2793593861926894e+01 6.4571740367787598e+01 -2.1289279778598913e+00
2 -1.2829292312064029e+01 -5.4533055036423278e+01 1.8187434445669542e+01
3 -2.4856613953429456e+01 1.0514866674084597e+02 -2.3296287600437509e+01
4 5.3912586948208610e+00 -1.9207748493955110e+00 -3.0737420829610784e+01
5 2.2876420006755072e+01 1.3823836581860232e+02 2.7754672239203551e+01
6 3.2990987866655288e+01 4.7389376657311274e+01 4.1925550028130715e-01
7 -5.3127337737189976e+01 7.9068725922500050e+01 3.3313480295224882e+00
8 -3.3776815354713030e+01 -3.1883796291469537e+01 3.1197870995948911e+01
9 -1.6142958936642351e+01 -5.6081173595531077e+01 -3.9752773026105103e+01
10 -2.3444945461170079e+01 -8.6264628791048494e+01 -9.7382848626466640e+01
11 -3.7845977091330013e+01 -8.9150810223199585e+01 5.7663720237686718e+01
12 3.0195173959030388e+00 -8.0980830765493238e+01 1.3208578723692574e+01
13 1.4074145069219668e+00 1.6274921833661661e+01 -3.2622589971920675e+01
14 3.4107233289225746e+01 -9.9470010392150936e+00 3.5127602437573628e+01
15 -2.5283377148309391e+01 1.4403149632708308e+01 -4.5870071592016277e+00
16 1.1347792324200792e+02 -8.2148516354961487e+01 3.6846638005266399e+01
17 3.9601805292343890e+01 1.0338789002649486e+02 1.9982264609004446e+01
18 -7.0147350906383394e+01 -1.9416536628860054e+01 -3.1061364649276509e+01
19 -8.0113796208824880e+01 -3.6203470152188125e+01 1.7073669110420070e+01
20 1.9118534843395143e+01 1.8040139592039122e+01 -2.5670655740910352e+01
21 1.0678029830913370e+02 8.4131852942169118e+01 2.5233622309511127e+01
22 -6.1256398451879237e+00 -4.5897733307809965e+01 -7.6777005140719412e+00
23 3.5851086965813614e+01 7.2727642790340141e+01 -8.3728640107852527e+01
24 5.7040471090952735e+01 5.0540340852012491e+01 3.9578738566151387e+01
25 3.4502137563453971e+01 1.0646154765045129e+01 -2.2629894541123310e+01
26 -4.8073017653735285e+01 -1.0752340517338715e+02 1.1113490074292022e+02
27 1.1423747645119571e+01 -2.4217562070846903e+01 -1.6319043178767714e+01
28 -8.1060220093085604e+00 2.0590140270631622e+01 3.1642408010462596e+01
29 2.6452264513660189e+01 5.1030856603567926e+01 -4.1657860341522763e+00
30 -2.3924536059677859e+01 -2.6294734320754202e+01 -3.9690770192486717e+01
31 -2.4704253734618757e+00 -5.6516273903220871e+01 2.5013410902961631e+01
32 -1.1056658903666158e+02 -6.7209662311912936e+01 -3.1944424716033090e+01
run_vdwl: 40769.6664263014
1 3.2793593861936280e+01 6.4571740367786191e+01 -2.1289279778636163e+00
2 -1.2829292312061501e+01 -5.4533055036424464e+01 1.8187434445667130e+01
3 -2.4856613953427402e+01 1.0514866674084669e+02 -2.3296287600436642e+01
4 5.3912586948203929e+00 -1.9207748493940047e+00 -3.0737420829608666e+01
5 2.2876420006743409e+01 1.3823836581860061e+02 2.7754672239209391e+01
6 3.2990987866655523e+01 4.7389376657316596e+01 4.1925550027908387e-01
7 -5.3127337737191212e+01 7.9068725922509202e+01 3.3313480295298135e+00
8 -3.3776815354712845e+01 -3.1883796291468244e+01 3.1197870995950865e+01
9 -1.6142958936642923e+01 -5.6081173595533613e+01 -3.9752773026104350e+01
10 -2.3444945461172352e+01 -8.6264628791039939e+01 -9.7382848626468672e+01
11 -3.7845977091329949e+01 -8.9150810223205866e+01 5.7663720237687556e+01
12 3.0195173959076653e+00 -8.0980830765500230e+01 1.3208578723696517e+01
13 1.4074145069243595e+00 1.6274921833658944e+01 -3.2622589971917748e+01
14 3.4107233289226450e+01 -9.9470010392147152e+00 3.5127602437571689e+01
15 -2.5283377148310002e+01 1.4403149632707610e+01 -4.5870071592035568e+00
16 1.1347792324200839e+02 -8.2148516354959909e+01 3.6846638005263920e+01
17 3.9601805292341801e+01 1.0338789002649888e+02 1.9982264609006680e+01
18 -7.0147350906377682e+01 -1.9416536628861550e+01 -3.1061364649270551e+01
19 -8.0113796208824979e+01 -3.6203470152182334e+01 1.7073669110416827e+01
20 1.9118534843396901e+01 1.8040139592040173e+01 -2.5670655740915695e+01
21 1.0678029830912494e+02 8.4131852942166489e+01 2.5233622309511937e+01
22 -6.1256398451892737e+00 -4.5897733307809744e+01 -7.6777005140674586e+00
23 3.5851086965819654e+01 7.2727642790344731e+01 -8.3728640107858183e+01
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run_vdwl: 40769.6664263018
run_coul: 0
run_stress: ! |2-
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run_forces: ! |2
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...

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