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Merge pull request #3781 from akohlmey/collected-small-fixes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2023-06-08 22:03:23 -04:00
committed by GitHub
parent cbf062f383 4cad18a057
commit 54286ce4dd
41 changed files with 1097 additions and 396 deletions
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2
doc/src/Build_manual.rst
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@ -52,7 +52,7 @@ can be translated to different output format using the `Sphinx
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl/>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle(tm) readers) are supported. For that to work a
and MOBI (for Amazon Kindle readers) are supported. For that to work a
Python interpreter version 3.8 or later, the ``doxygen`` tools and
internet access to download additional files and tools are required.
This download is usually only required once or after the documentation

191
doc/src/Fortran.rst
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@ -203,40 +203,62 @@ Below is an example demonstrating some of the possible uses.
.. code-block:: fortran
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms
REAL(KIND=c_double), POINTER :: dt
INTEGER(KIND=c_int64_t), POINTER :: ntimestep
REAL(KIND=c_double) :: pe, ke
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
REAL(KIND=c_double), POINTER :: dt, dval
INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
INTEGER(KIND=c_int) :: i
CHARACTER(LEN=11) :: key
REAL(KIND=c_double) :: pe, ke
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
CALL lmp%command('run 2 post no')
dt = lmp%extract_global('dt')
ntimestep = lmp%extract_global('ntimestep')
WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
' Changing timestep from', dt, ' to 0.5'
dt = 0.5_c_double
CALL lmp%command('run 2 post no')
CALL lmp%command('run 2 post no')
WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
pe = lmp%get_thermo('pe')
ke = lmp%get_thermo('ke')
PRINT*, 'PE = ', pe
PRINT*, 'KE = ', ke
ntimestep = lmp%last_thermo('step', 0)
nfield = lmp%last_thermo('num', 0)
WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') 'Last thermo output on step: ', ntimestep, &
', number of fields: ', nfield
DO i=1, nfield
key = lmp%last_thermo('keyword',i)
typ = lmp%last_thermo('type',i)
IF (typ == lmp%dtype%i32) THEN
ival = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', ival
ELSE IF (typ == lmp%dtype%i64) THEN
bval = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', bval
ELSE IF (typ == lmp%dtype%r64) THEN
dval = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', dval
END IF
END DO
CALL lmp%close(.TRUE.)
END PROGRAM testprop
dt = lmp%extract_global('dt')
ntimestep = lmp%extract_global('ntimestep')
WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
' Changing timestep from', dt, ' to 0.5'
dt = 0.5_c_double
CALL lmp%command('run 2 post no')
WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
pe = lmp%get_thermo('pe')
ke = lmp%get_thermo('ke')
WRITE(OUTPUT_UNIT,*) 'PE = ', pe
WRITE(OUTPUT_UNIT,*) 'KE = ', ke
CALL lmp%close(.TRUE.)
END PROGRAM testprop
---------------
@ -262,6 +284,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype style: type(lammps_style)
:f type: derived type to access lammps type constants
:ftype type: type(lammps_type)
:f dtype: derived type to access lammps data type constants
:ftype dtype: type(lammps_dtype)
:f close: :f:subr:`close`
:ftype close: subroutine
:f subroutine error: :f:subr:`error`
@ -278,6 +302,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype get_natoms: function
:f get_thermo: :f:func:`get_thermo`
:ftype get_thermo: function
:f last_thermo: :f:func:`last_thermo`
:ftype last_thermo: function
:f extract_box: :f:subr:`extract_box`
:ftype extract_box: subroutine
:f reset_box: :f:subr:`reset_box`
@ -587,6 +613,96 @@ Procedures Bound to the :f:type:`lammps` Derived Type
--------
.. f:function:: last_thermo(what, index)
This function will call :cpp:func:`lammps_last_thermo` and returns
either a string or a pointer to a cached copy of LAMMPS last thermodynamic
output, depending on the data requested through *what*. Note that *index*
uses 1-based indexing to access thermo output columns.
.. versionadded:: TBD
Note that this function actually does not return a value, but rather
associates the pointer on the left side of the assignment to point to
internal LAMMPS data (with the exception of string data, which are
copied and returned as ordinary Fortran strings). Pointers must be
of the correct data type to point to said data (typically
``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``).
The pointer being associated with LAMMPS data is type-checked at
run-time via an overloaded assignment operator. The pointers
returned by this function point to temporary, read-only data that may
be overwritten at any time, so their target values need to be copied
to local storage if they are supposed to persist.
For example,
.. code-block:: fortran
PROGRAM thermo
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval
REAL(KIND=c_double), POINTER :: dval
INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
INTEGER(KIND=c_int) :: i
CHARACTER(LEN=11) :: key
lmp = lammps()
CALL lmp%file('in.sysinit')
ntimestep = lmp%last_thermo('step', 0)
nfield = lmp%last_thermo('num', 0)
PRINT*, 'Last thermo output on step: ', ntimestep, ' Number of fields: ', nfield
DO i=1, nfield
key = lmp%last_thermo('keyword',i)
typ = lmp%last_thermo('type',i)
IF (typ == lmp%dtype%i32) THEN
ival = lmp%last_thermo('data',i)
PRINT*, key, ':', ival
ELSE IF (typ == lmp%dtype%i64) THEN
bval = lmp%last_thermo('data',i)
PRINT*, key, ':', bval
ELSE IF (typ == lmp%dtype%r64) THEN
dval = lmp%last_thermo('data',i)
PRINT*, key, ':', dval
END IF
END DO
CALL lmp%close(.TRUE.)
END PROGRAM thermo
would extract the last timestep where thermo output was done and the number
of columns it printed. Then it loops over the columns to print out column
header keywords and the corresponding data.
.. note::
If :f:func:`last_thermo` returns a string, the string must have a length
greater than or equal to the length of the string (not including the
terminal ``NULL`` character) that LAMMPS returns. If the variable's
length is too short, the string will be truncated. As usual in Fortran,
strings are padded with spaces at the end. If you use an allocatable
string, the string **must be allocated** prior to calling this function.
:p character(len=\*) what: string with the name of the thermo keyword
:p integer(c_int) index: 1-based column index
:to: :cpp:func:`lammps_last_thermo`
:r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the
assignment should be either a string (if expecting string data) or a
C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the
extracted property.
.. warning::
Modifying the data in the location pointed to by the returned pointer
may lead to inconsistent internal data and thus may cause failures,
crashes, or bogus simulations. In general, it is much better
to use a LAMMPS input command that sets or changes these parameters.
Using an input command will take care of all side effects and necessary
updates of settings derived from such settings.
--------
.. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
This subroutine will call :cpp:func:`lammps_extract_box`. All
@ -764,13 +880,14 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. note::
If :f:func:`extract_global` returns a string, the string must have length
greater than or equal to the length of the string (not including the
terminal ``NULL`` character) that LAMMPS returns. If the variable's
length is too short, the string will be truncated. As usual in Fortran,
strings are padded with spaces at the end. If you use an allocatable
string, the string **must be allocated** prior to calling this function,
but you can automatically reallocate it to the correct length after the
If :f:func:`extract_global` returns a string, the string must have
a length greater than or equal to the length of the string (not
including the terminal ``NULL`` character) that LAMMPS returns. If
the variable's length is too short, the string will be
truncated. As usual in Fortran, strings are padded with spaces at
the end. If you use an allocatable string, the string **must be
allocated** prior to calling this function, but you can
automatically reallocate it to the correct length after the
function returns, viz.,
.. code-block :: fortran

6
doc/src/Howto_spc.rst
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@ -69,15 +69,13 @@ SPC/E with rigid bonds.
timestep 1.0
fix rigid all shake 0.0001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
velocity all create 300.0 5463576
fix integrate all nvt temp 300.0 300.0 1.0
fix integrate all nvt temp 300.0 300.0 100.0
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000 upto
write_data tip4p.data nocoeff
write_data spce.data nocoeff
.. _spce_molecule:
.. code-block::

4
doc/src/Howto_tip3p.rst
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@ -128,11 +128,11 @@ TIP3P with rigid bonds.
fix rigid all shake 0.001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
timestep 1.0
velocity all create 300.0 5463576
fix integrate all nvt temp 300 300 1.0
fix integrate all nvt temp 300 300 100.0
thermo_style custom step temp press etotal pe

13
doc/src/Howto_tip4p.rst
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@ -180,17 +180,17 @@ file changed):
fix rigid all shake 0.001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
timestep 1.0
velocity all create 300.0 5463576
fix integrate all nvt temp 300 300 1.0
fix integrate all nvt temp 300 300 100.0
thermo_style custom step temp press etotal pe
thermo 1000
run 20000
write_data tip3p.data nocoeff
write_data tip4p-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small
@ -203,6 +203,7 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
units real
atom_style charge
atom_modify map array
region box block -5 5 -5 5 -5 5
create_box 3 box
@ -219,14 +220,14 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
timestep 0.1
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000
write_data tip4p.data nocoeff
write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule:
.. code-block::

5
doc/src/Howto_tip5p.rst
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@ -91,6 +91,7 @@ ID:
units real
atom_style charge
atom_modify map array
region box block -5 5 -5 5 -5 5
create_box 3 box
@ -107,8 +108,8 @@ ID:
molecule water tip5p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
timestep 0.20
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
reset_timestep 0
velocity all create 300.0 5463576

6
doc/src/Library_properties.rst
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@ -5,6 +5,7 @@ This section documents the following functions:
- :cpp:func:`lammps_get_natoms`
- :cpp:func:`lammps_get_thermo`
- :cpp:func:`lammps_last_thermo`
- :cpp:func:`lammps_extract_box`
- :cpp:func:`lammps_reset_box`
- :cpp:func:`lammps_memory_usage`
@ -81,6 +82,11 @@ subdomains and processors.
-----------------------
.. doxygenfunction:: lammps_last_thermo
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_box
:project: progguide

10
doc/src/dump_modify.rst
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@ -753,9 +753,13 @@ run, this option is ignored since the output is already balanced.
----------
The *thermo* keyword only applies the dump styles *netcdf* and *yaml*.
It triggers writing of :doc:`thermo <thermo>` information to the dump file
alongside per-atom data. The values included in the dump file are
identical to the values specified by :doc:`thermo_style <thermo_style>`.
It triggers writing of :doc:`thermo <thermo>` information to the dump
file alongside per-atom data. The values included in the dump file are
cached values from the last thermo output and include the exact same the
values as specified by the :doc:`thermo_style <thermo_style>` command.
Because these are cached values, they are only up-to-date when dump
output is on a timestep that also has thermo output. Dump style *yaml*
will skip thermo output on incompatible steps.
----------

23
doc/src/fix_reaxff_species.rst
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@ -25,7 +25,7 @@ Syntax
.. parsed-literal::
*cutoff* value = I J Cutoff
I, J = atom types
I, J = atom types (see asterisk form below)
Cutoff = Bond-order cutoff value for this pair of atom types
*element* value = Element1, Element2, ...
*position* value = posfreq filepos
@ -49,7 +49,7 @@ Examples
.. code-block:: LAMMPS
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
@ -88,13 +88,24 @@ If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text version,
but will also take longer to write.
.. versionadded:: TBD
Support for wildcards added
Optional keyword *cutoff* can be assigned to change the minimum
bond-order values used in identifying chemical bonds between pairs of
atoms. Bond-order cutoffs should be carefully chosen, as bond-order
cutoffs that are too small may include too many bonds (which will
result in an error), while cutoffs that are too large will result in
fragmented molecules. The default cutoff of 0.3 usually gives good
results.
cutoffs that are too small may include too many bonds (which will result
in an error), while cutoffs that are too large will result in fragmented
molecules. The default cutoff of 0.3 usually gives good results. A
wildcard asterisk can be used in place of or in conjunction with the I,J
arguments to set the bond-order cutoff for multiple pairs of atom types.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If :math:`N` is
the number of atom types, then an asterisk with no numeric values means
all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
The optional keyword *element* can be used to specify the chemical
symbol printed for each LAMMPS atom type. The number of symbols must

2
doc/src/variable.rst
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@ -1481,7 +1481,7 @@ commands
.. code-block:: LAMMPS
# delete_atoms random fraction 0.5 yes all NULL 49839
# run 0
# run 0 post no
variable t equal temp # this thermo keyword invokes a temperature compute
print "Temperature of system = $t"
run 1000

1
doc/utils/sphinx-config/false_positives.txt
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@ -3742,6 +3742,7 @@ Umin
un
unary
uncomment
uncommented
uncompress
uncompute
underprediction

1
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -90,6 +90,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(get_natoms);
ADDSYM(get_thermo);
ADDSYM(last_thermo);
ADDSYM(extract_box);
ADDSYM(reset_box);

1
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -133,6 +133,7 @@ struct _liblammpsplugin {
double (*get_natoms)(void *);
double (*get_thermo)(void *, const char *);
void *(*last_thermo)(void *, const char *, int);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);

80
fortran/lammps.f90
View File

@ -87,10 +87,15 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: scalar, vector, array
END TYPE lammps_type
TYPE lammps_dtype
INTEGER(c_int) :: i32, i64, r64, str
END TYPE lammps_dtype
TYPE lammps
TYPE(c_ptr) :: handle = c_null_ptr
TYPE(lammps_style) :: style
TYPE(lammps_type) :: type
TYPE(lammps_dtype) :: dtype
CONTAINS
PROCEDURE :: close => lmp_close
PROCEDURE :: error => lmp_error
@ -100,6 +105,7 @@ MODULE LIBLAMMPS
PROCEDURE :: commands_string => lmp_commands_string
PROCEDURE :: get_natoms => lmp_get_natoms
PROCEDURE :: get_thermo => lmp_get_thermo
PROCEDURE :: last_thermo => lmp_last_thermo
PROCEDURE :: extract_box => lmp_extract_box
PROCEDURE :: reset_box => lmp_reset_box
PROCEDURE :: memory_usage => lmp_memory_usage
@ -243,7 +249,7 @@ MODULE LIBLAMMPS
END TYPE lammps_data_baseclass
! Derived type for receiving LAMMPS data (in lieu of the ability to type cast
! pointers). Used for extract_compute, extract_atom
! pointers). Used for extract_compute, extract_atom, last_thermo
TYPE, EXTENDS(lammps_data_baseclass) :: lammps_data
INTEGER(c_int), POINTER :: i32 => NULL()
INTEGER(c_int), DIMENSION(:), POINTER :: i32_vec => NULL()
@ -439,6 +445,15 @@ MODULE LIBLAMMPS
TYPE(c_ptr), INTENT(IN), VALUE :: name
END FUNCTION lammps_get_thermo
FUNCTION lammps_last_thermo(handle,what,index) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr) :: lammps_last_thermo
TYPE(c_ptr), INTENT(IN), VALUE :: handle
TYPE(c_ptr), INTENT(IN), VALUE :: what
INTEGER(c_int), INTENT(IN), VALUE :: index
END FUNCTION lammps_last_thermo
SUBROUTINE lammps_extract_box(handle,boxlo,boxhi,xy,yz,xz,pflags, &
boxflag) BIND(C)
IMPORT :: c_ptr, c_double, c_int
@ -995,6 +1010,10 @@ CONTAINS
lmp_open%type%scalar = LMP_TYPE_SCALAR
lmp_open%type%vector = LMP_TYPE_VECTOR
lmp_open%type%array = LMP_TYPE_ARRAY
lmp_open%dtype%i32 = LAMMPS_INT
lmp_open%dtype%i64 = LAMMPS_INT64
lmp_open%dtype%r64 = LAMMPS_DOUBLE
lmp_open%dtype%str = LAMMPS_STRING
! Assign constants for bigint and tagint for use elsewhere
SIZE_TAGINT = lmp_extract_setting(lmp_open, 'tagint')
@ -1103,6 +1122,65 @@ CONTAINS
CALL lammps_free(Cname)
END FUNCTION lmp_get_thermo
! equivalent function to lammps_last_thermo
FUNCTION lmp_last_thermo(self,what,index) RESULT(thermo_data)
CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: what
INTEGER(c_int) :: index
TYPE(lammps_data) :: thermo_data, type_data
INTEGER(c_int) :: datatype
TYPE(c_ptr) :: Cname, Cptr
! set data type for known cases
SELECT CASE (what)
CASE ('step')
IF (SIZE_BIGINT == 4_c_int) THEN
datatype = LAMMPS_INT
ELSE
datatype = LAMMPS_INT64
END IF
CASE ('num')
datatype = LAMMPS_INT
CASE ('type')
datatype = LAMMPS_INT
CASE ('keyword')
datatype = LAMMPS_STRING
CASE ('data')
Cname = f2c_string('type')
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
type_data%lammps_instance => self
type_data%datatype = DATA_INT
CALL C_F_POINTER(Cptr, type_data%i32)
datatype = type_data%i32
CALL lammps_free(Cname)
CASE DEFAULT
datatype = -1
END SELECT
Cname = f2c_string(what)
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
CALL lammps_free(Cname)
thermo_data%lammps_instance => self
SELECT CASE (datatype)
CASE (LAMMPS_INT)
thermo_data%datatype = DATA_INT
CALL C_F_POINTER(Cptr, thermo_data%i32)
CASE (LAMMPS_INT64)
thermo_data%datatype = DATA_INT64
CALL C_F_POINTER(Cptr, thermo_data%i64)
CASE (LAMMPS_DOUBLE)
thermo_data%datatype = DATA_DOUBLE
CALL C_F_POINTER(Cptr, thermo_data%r64)
CASE (LAMMPS_STRING)
thermo_data%datatype = DATA_STRING
thermo_data%str = c2f_string(Cptr)
CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'Unknown pointer type in last_thermo')
END SELECT
END FUNCTION lmp_last_thermo
! equivalent subroutine to lammps_extract_box
SUBROUTINE lmp_extract_box(self, boxlo, boxhi, xy, yz, xz, pflags, boxflag)
CLASS(lammps), INTENT(IN) :: self

124
python/lammps/core.py
View File

@ -272,6 +272,9 @@ class lammps(object):
self.lib.lammps_get_thermo.argtypes = [c_void_p, c_char_p]
self.lib.lammps_get_thermo.restype = c_double
self.lib.lammps_last_thermo.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_last_thermo.restype = c_void_p
self.lib.lammps_encode_image_flags.restype = self.c_imageint
self.lib.lammps_config_has_package.argtypes = [c_char_p]
@ -503,9 +506,9 @@ class lammps(object):
def error(self, error_type, error_text):
"""Forward error to the LAMMPS Error class.
This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
.. versionadded:: 3Nov2022
.. versionadded:: TBD
This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
:param error_type:
:type error_type: int
@ -744,6 +747,56 @@ class lammps(object):
# -------------------------------------------------------------------------
def last_thermo(self):
"""Get a dictionary of the last thermodynamic output
This is a wrapper around the :cpp:func:`lammps_last_thermo`
function of the C-library interface. It collects the cached thermo
data from the last timestep into a dictionary. The return value
is None, if there has not been any thermo output yet.
:return: value of thermo keyword
:rtype: dict or None
"""
rv = dict()
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
mystep = cast(ptr, POINTER(self.c_bigint)).contents.value
if mystep < 0:
return None
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("num".encode()), 0)
nfield = cast(ptr, POINTER(c_int)).contents.value
for i in range(nfield):
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("keyword".encode()), i)
kw = cast(ptr, c_char_p).value.decode()
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
typ = cast(ptr, POINTER(c_int)).contents.value
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("data".encode()), i)
if typ == LAMMPS_DOUBLE:
val = cast(ptr, POINTER(c_double)).contents.value
elif typ == LAMMPS_INT:
val = cast(ptr, POINTER(c_int)).contents.value
elif typ == LAMMPS_INT64:
val = cast(ptr, POINTER(c_int64)).contents.value
else:
# we should not get here
raise TypeError("Unknown LAMMPS data type " + str(typ))
rv[kw] = val
return rv
# -------------------------------------------------------------------------
def extract_setting(self, name):
"""Query LAMMPS about global settings that can be expressed as an integer.
@ -1289,6 +1342,8 @@ class lammps(object):
def gather_bonds(self):
"""Retrieve global list of bonds
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_gather_bonds`
function of the C-library interface.
@ -1296,8 +1351,6 @@ class lammps(object):
flat list of ctypes integer values with the bond type, bond atom1,
bond atom2 for each bond.
.. versionadded:: 28Jul2021
:return: a tuple with the number of bonds and a list of c_int or c_long
:rtype: (int, 3*nbonds*c_tagint)
"""
@ -1312,6 +1365,8 @@ class lammps(object):
def gather_angles(self):
"""Retrieve global list of angles
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_angles`
function of the C-library interface.
@ -1319,8 +1374,6 @@ class lammps(object):
flat list of ctypes integer values with the angle type, angle atom1,
angle atom2, angle atom3 for each angle.
.. versionadded:: TBD
:return: a tuple with the number of angles and a list of c_int or c_long
:rtype: (int, 4*nangles*c_tagint)
"""
@ -1335,6 +1388,8 @@ class lammps(object):
def gather_dihedrals(self):
"""Retrieve global list of dihedrals
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_dihedrals`
function of the C-library interface.
@ -1342,8 +1397,6 @@ class lammps(object):
flat list of ctypes integer values with the dihedral type, dihedral atom1,
dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.
.. versionadded:: TBD
:return: a tuple with the number of dihedrals and a list of c_int or c_long
:rtype: (int, 5*ndihedrals*c_tagint)
"""
@ -1358,6 +1411,8 @@ class lammps(object):
def gather_impropers(self):
"""Retrieve global list of impropers
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_impropers`
function of the C-library interface.
@ -1365,8 +1420,6 @@ class lammps(object):
flat list of ctypes integer values with the improper type, improper atom1,
improper atom2, improper atom3, improper atom4 for each improper.
.. versionadded:: TBD
:return: a tuple with the number of impropers and a list of c_int or c_long
:rtype: (int, 5*nimpropers*c_tagint)
"""
@ -1605,13 +1658,13 @@ class lammps(object):
def is_running(self):
""" Report whether being called from a function during a run or a minimization
.. versionadded:: 9Oct2020
Various LAMMPS commands must not be called during an ongoing
run or minimization. This property allows to check for that.
This is a wrapper around the :cpp:func:`lammps_is_running`
function of the library interface.
.. versionadded:: 9Oct2020
:return: True when called during a run otherwise false
:rtype: bool
"""
@ -1622,12 +1675,13 @@ class lammps(object):
def force_timeout(self):
""" Trigger an immediate timeout, i.e. a "soft stop" of a run.
.. versionadded:: 9Oct2020
This function allows to cleanly stop an ongoing run or minimization
at the next loop iteration.
This is a wrapper around the :cpp:func:`lammps_force_timeout`
function of the library interface.
.. versionadded:: 9Oct2020
"""
self.lib.lammps_force_timeout(self.lmp)
@ -1710,11 +1764,11 @@ class lammps(object):
def has_package(self, name):
""" Report if the named package has been enabled in the LAMMPS shared library.
.. versionadded:: 3Nov2022
This is a wrapper around the :cpp:func:`lammps_config_has_package`
function of the library interface.
.. versionadded:: TBD
:param name: name of the package
:type name: string
@ -1854,11 +1908,11 @@ class lammps(object):
def has_id(self, category, name):
"""Returns whether a given ID name is available in a given category
.. versionadded:: 9Oct2020
This is a wrapper around the function :cpp:func:`lammps_has_id`
of the library interface.
.. versionadded:: 9Oct2020
:param category: name of category
:type category: string
:param name: name of the ID
@ -1874,11 +1928,11 @@ class lammps(object):
def available_ids(self, category):
"""Returns a list of IDs available for a given category
.. versionadded:: 9Oct2020
This is a wrapper around the functions :cpp:func:`lammps_id_count()`
and :cpp:func:`lammps_id_name()` of the library interface.
.. versionadded:: 9Oct2020
:param category: name of category
:type category: string
@ -1901,11 +1955,11 @@ class lammps(object):
def available_plugins(self, category):
"""Returns a list of plugins available for a given category
.. versionadded:: 10Mar2021
This is a wrapper around the functions :cpp:func:`lammps_plugin_count()`
and :cpp:func:`lammps_plugin_name()` of the library interface.
.. versionadded:: 10Mar2021
:return: list of style/name pairs of loaded plugins
:rtype: list
"""
@ -1970,11 +2024,11 @@ class lammps(object):
def fix_external_get_force(self, fix_id):
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -1989,11 +2043,11 @@ class lammps(object):
def fix_external_set_energy_global(self, fix_id, eng):
"""Set the global energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: potential energy value to be added by fix external
@ -2008,11 +2062,11 @@ class lammps(object):
def fix_external_set_virial_global(self, fix_id, virial):
"""Set the global virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: list of 6 floating point numbers with the virial to be added by fix external
@ -2028,11 +2082,11 @@ class lammps(object):
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the per-atom energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: list of potential energy values for local atoms to be added by fix external
@ -2051,11 +2105,11 @@ class lammps(object):
def fix_external_set_virial_peratom(self, fix_id, vatom):
"""Set the per-atom virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param vatom: list of natoms lists with 6 floating point numbers to be added by fix external
@ -2083,11 +2137,11 @@ class lammps(object):
def fix_external_set_vector_length(self, fix_id, length):
"""Set the vector length for a global vector stored with fix external for analysis
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param length: length of the global vector
@ -2101,11 +2155,11 @@ class lammps(object):
def fix_external_set_vector(self, fix_id, idx, val):
"""Store a global vector value for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param idx: 1-based index of the value in the global vector

28
python/lammps/numpy_wrapper.py
View File

@ -262,12 +262,12 @@ class numpy_wrapper:
def gather_bonds(self):
"""Retrieve global list of bonds as NumPy array
.. versionadded:: 28Jul2021
This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: 28Jul2021
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nbonds,3)
"""
@ -280,12 +280,12 @@ class numpy_wrapper:
def gather_angles(self):
""" Retrieve global list of angles as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nangles,4)
"""
@ -298,12 +298,12 @@ class numpy_wrapper:
def gather_dihedrals(self):
""" Retrieve global list of dihedrals as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(ndihedrals,5)
"""
@ -316,12 +316,12 @@ class numpy_wrapper:
def gather_impropers(self):
""" Retrieve global list of impropers as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nimpropers,5)
"""
@ -334,13 +334,13 @@ class numpy_wrapper:
def fix_external_get_force(self, fix_id):
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
.. versionchanged:: 28Jul2021
This function is a wrapper around the
:py:meth:`lammps.fix_external_get_force() <lammps.lammps.fix_external_get_force()>`
method. It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` pointer.
.. versionchanged:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -356,13 +356,13 @@ class numpy_wrapper:
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the per-atom energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This function is an alternative to
:py:meth:`lammps.fix_external_set_energy_peratom() <lammps.lammps.fix_external_set_energy_peratom()>`
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy
@ -383,13 +383,13 @@ class numpy_wrapper:
def fix_external_set_virial_peratom(self, fix_id, vatom):
"""Set the per-atom virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This function is an alternative to
:py:meth:`lammps.fix_external_set_virial_peratom() <lammps.lammps.fix_external_set_virial_peratom()>`
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy

3
src/DIFFRACTION/compute_xrd.cpp
View File

@ -90,8 +90,7 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
ztype[i] = j;
}
}
if (ztype[i] == XRDmaxType + 1)
error->all(FLERR,"Compute XRD: Invalid ASF atom type");
if (ztype[i] == XRDmaxType + 1) error->all(FLERR,"Compute XRD: Invalid ASF atom type {}", arg[iarg]);
iarg++;
}

36
src/EXTRA-DUMP/dump_yaml.cpp
View File

@ -60,21 +60,29 @@ void DumpYAML::write_header(bigint ndump)
std::string thermo_data;
if (thermo) {
Thermo *th = output->thermo;
thermo_data += "thermo:\n - keywords: [ ";
for (int i = 0; i < th->nfield; ++i) thermo_data += fmt::format("{}, ", th->keyword[i]);
thermo_data += "]\n - data: [ ";
// output thermo data only on timesteps where it was computed
if (update->ntimestep == *th->get_timestep()) {
int nfield = *th->get_nfield();
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
for (int i = 0; i < th->nfield; ++i) {
th->call_vfunc(i);
if (th->vtype[i] == Thermo::FLOAT)
thermo_data += fmt::format("{}, ", th->dvalue);
else if (th->vtype[i] == Thermo::INT)
thermo_data += fmt::format("{}, ", th->ivalue);
else if (th->vtype[i] == Thermo::BIGINT)
thermo_data += fmt::format("{}, ", th->bivalue);
thermo_data += "thermo:\n - keywords: [ ";
for (int i = 0; i < nfield; ++i) thermo_data += fmt::format("{}, ", keywords[i]);
thermo_data += "]\n - data: [ ";
for (int i = 0; i < nfield; ++i) {
if (fields[i].type == multitype::DOUBLE)
thermo_data += fmt::format("{}, ", fields[i].data.d);
else if (fields[i].type == multitype::INT)
thermo_data += fmt::format("{}, ", fields[i].data.i);
else if (fields[i].type == multitype::BIGINT)
thermo_data += fmt::format("{}, ", fields[i].data.b);
else
thermo_data += ", ";
}
thermo_data += "]\n";
MPI_Barrier(world);
}
thermo_data += "]\n";
MPI_Barrier(world);
}
if (comm->me == 0) {
@ -85,7 +93,7 @@ void DumpYAML::write_header(bigint ndump)
fmt::print(fp, "natoms: {}\n", ndump);
fputs("boundary: [ ", fp);
for (const auto bflag : boundary) {
for (const auto &bflag : boundary) {
if (bflag == ' ') continue;
fmt::print(fp, "{}, ", bflag);
}

3
src/EXTRA-FIX/fix_electron_stopping.cpp
View File

@ -175,7 +175,8 @@ void FixElectronStopping::post_force(int /*vflag*/)
if (energy < Ecut) continue;
if (energy < elstop_ranges[0][0]) continue;
if (energy > elstop_ranges[0][table_entries - 1])
error->one(FLERR, "Atom kinetic energy too high for fix electron/stopping");
error->one(FLERR, "Fix electron/stopping: kinetic energy too high for atom {}: {} vs {}",
atom->tag[i], energy, elstop_ranges[0][table_entries - 1]);
if (region) {
// Only apply in the given region

6
src/GRANULAR/gran_sub_mod_normal.h
View File

@ -94,7 +94,7 @@ namespace Granular_NS {
void coeffs_to_local() override;
void mix_coeffs(double *, double *) override;
private:
int mixed_coefficients;
int mixed_coefficients;
};
/* ---------------------------------------------------------------------- */
@ -110,7 +110,7 @@ namespace Granular_NS {
protected:
double k, cohesion;
double F_pulloff, Fne;
int mixed_coefficients;
int mixed_coefficients;
};
/* ---------------------------------------------------------------------- */
@ -129,7 +129,7 @@ namespace Granular_NS {
protected:
double k, cohesion;
double Emix, F_pulloff, Fne;
int mixed_coefficients;
int mixed_coefficients;
};
} // namespace Granular_NS

4
src/KOKKOS/comm_kokkos.cpp
View File

@ -980,9 +980,9 @@ void CommKokkos::borders()
} else {
atomKK->sync(Host,ALL_MASK);
k_sendlist.sync<LMPHostType>();
CommBrick::borders();
k_sendlist.modify<LMPHostType>();
atomKK->modified(Host,ALL_MASK);
atomKK->modified(Host,ALL_MASK); // needed here for atom map
CommBrick::borders();
}
if (comm->nprocs == 1 && !ghost_velocity && !forward_comm_classic)

71
src/NETCDF/dump_netcdf.cpp
View File

@ -195,6 +195,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
type_nc_real = NC_FLOAT;
thermo = false;
thermo_warn = true;
thermovar = nullptr;
framei = 0;
@ -223,7 +224,7 @@ void DumpNetCDF::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -321,8 +322,11 @@ void DumpNetCDF::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
NCERRX( nc_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
}
}
@ -433,21 +437,17 @@ void DumpNetCDF::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
#else
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
#endif
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
}
@ -606,19 +606,30 @@ void DumpNetCDF::write()
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
th->call_vfunc(i);
// will output current thermo data only on timesteps where it was computed.
// warn (once) about using cached copy from old timestep.
if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
thermo_warn = false;
if (comm->me == 0) {
error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
" Dump netcdf always stores thermo data from last thermo output",
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
&th->dvalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i].c_str() );
if (fields[i].type == multitype::DOUBLE) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}
}

1
src/NETCDF/dump_netcdf.h
View File

@ -65,6 +65,7 @@ class DumpNetCDF : public DumpCustom {
int type_nc_real; // netcdf type to use for real variables: float or double
bool thermo; // write thermo output to netcdf file
bool thermo_warn; // warn (once) that thermo output is on incompatible step
bigint n_buffer; // size of buffer
bigint *int_buffer; // buffer for passing data to netcdf

69
src/NETCDF/dump_netcdf_mpiio.cpp
View File

@ -192,6 +192,7 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
type_nc_real = NC_FLOAT;
thermo = false;
thermo_warn = true;
thermovar = nullptr;
framei = 0;
@ -220,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -319,8 +320,11 @@ void DumpNetCDFMPIIO::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
NCERRX( ncmpi_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
}
}
@ -423,17 +427,17 @@ void DumpNetCDFMPIIO::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
#else
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
#endif
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
}
@ -595,25 +599,36 @@ void DumpNetCDFMPIIO::write()
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
th->call_vfunc(i);
// will output current thermo data only on timesteps where it was computed.
// warn (once) about using cached copy from old timestep.
if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
thermo_warn = false;
if (comm->me == 0) {
error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
" Dump netcdf/mpiio always stores thermo data from last thermo output",
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start,
&th->dvalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i].c_str() );
if (fields[i].type == multitype::DOUBLE) {
NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}
}
}
// write timestep header
// write timestep header
write_time_and_cell();

1
src/NETCDF/dump_netcdf_mpiio.h
View File

@ -62,6 +62,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
int type_nc_real; // netcdf type to use for real variables: float or double
bool thermo; // write thermo output to netcdf file
bool thermo_warn; // warn (once) that thermo output is on incompatible step
bigint n_buffer; // size of buffer
bigint *int_buffer; // buffer for passing data to netcdf

106
src/REAXFF/fix_reaxff_species.cpp
View File

@ -48,15 +48,16 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_reaxff_species_delete[] =
"fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
"@Article{Gissinger23,\n"
" author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. Odegard, E. J. Siochi, K. E. Wise},\n"
" title = {Predicting char yield of high-temperature resins},\n"
" journal = {Carbon},\n"
" year = 2023,\n"
" volume = 202,\n"
" pages = {336-347}\n"
"}\n\n";
"fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
"@Article{Gissinger23,\n"
" author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. "
"Odegard, E. J. Siochi, K. E. Wise},\n"
" title = {Predicting char yield of high-temperature resins},\n"
" journal = {Carbon},\n"
" year = 2023,\n"
" volume = 202,\n"
" pages = {336-347}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -148,13 +149,11 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
setupflag = 0;
// set default bond order cutoff
int itype, jtype;
double bo_cut;
bg_cut = 0.30;
double bo_cut = 0.30;
int np1 = ntypes + 1;
memory->create(BOCut, np1, np1, "reaxff/species:BOCut");
for (int i = 1; i < np1; i++)
for (int j = 1; j < np1; j++) BOCut[i][j] = bg_cut;
for (int j = 1; j < np1; j++) BOCut[i][j] = bo_cut;
// optional args
eletype = nullptr;
@ -172,16 +171,19 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
// set BO cutoff
if (strcmp(arg[iarg], "cutoff") == 0) {
if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species cutoff", error);
itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
jtype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[iarg + 1], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[iarg + 2], 1, atom->ntypes, jlo, jhi, error);
bo_cut = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
if ((itype <= 0) || (jtype <= 0) || (itype > ntypes) || (jtype > ntypes))
error->all(FLERR, "Fix reaxff/species cutoff atom type(s) out of range");
if ((bo_cut > 1.0) || (bo_cut < 0.0))
error->all(FLERR, "Fix reaxff/species invalid cutoff value: {}", bo_cut);
BOCut[itype][jtype] = bo_cut;
BOCut[jtype][itype] = bo_cut;
for (int i = ilo; i <= ihi; ++i) {
for (int j = MAX(jlo, i); j <= jhi; ++j) {
BOCut[i][j] = bo_cut;
BOCut[j][i] = bo_cut;
}
}
iarg += 4;
// modify element type names
@ -240,17 +242,21 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR, "Unknown fix reaxff/species delete option: {}", arg[iarg]);
// rate limit when deleting molecules
} else if (strcmp(arg[iarg], "delete_rate_limit") == 0) {
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
if (iarg + 3 > narg)
utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
delete_Nlimit_varid = -1;
if (strncmp(arg[iarg+1],"v_",2) == 0) {
delete_Nlimit_varname = &arg[iarg+1][2];
if (strncmp(arg[iarg + 1], "v_", 2) == 0) {
delete_Nlimit_varname = &arg[iarg + 1][2];
delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
if (delete_Nlimit_varid < 0)
error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
delete_Nlimit_varname);
if (!input->variable->equalstyle(delete_Nlimit_varid))
error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
} else delete_Nlimit = utils::numeric(FLERR, arg[iarg+1], false, lmp);
delete_Nsteps = utils::numeric(FLERR, arg[iarg+2], false, lmp);
error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
delete_Nlimit_varname);
} else
delete_Nlimit = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
delete_Nsteps = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
iarg += 3;
// position of molecules
} else if (strcmp(arg[iarg], "position") == 0) {
@ -292,10 +298,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
if (delete_Nsteps > 0) {
if (lmp->citeme) lmp->citeme->add(cite_reaxff_species_delete);
memory->create(delete_Tcount,delete_Nsteps,"reaxff/species:delete_Tcount");
memory->create(delete_Tcount, delete_Nsteps, "reaxff/species:delete_Tcount");
for (int i = 0; i < delete_Nsteps; i++)
delete_Tcount[i] = -1;
for (int i = 0; i < delete_Nsteps; i++) delete_Tcount[i] = -1;
delete_Tcount[0] = 0;
}
@ -393,9 +398,11 @@ void FixReaxFFSpecies::init()
if (delete_Nsteps > 0) {
delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
if (delete_Nlimit_varid < 0)
error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
delete_Nlimit_varname);
if (!input->variable->equalstyle(delete_Nlimit_varid))
error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
delete_Nlimit_varname);
}
}
@ -427,8 +434,7 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
if (ntimestep != nvalid) {
// push back delete_Tcount on every step
if (delete_Nsteps > 0)
for (int i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
for (int i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
return;
}
@ -732,31 +738,31 @@ void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec)
int i, j, itemp;
bigint ntimestep = update->ntimestep;
fprintf(fp, "# Timestep No_Moles No_Specs ");
fprintf(fp, "# Timestep No_Moles No_Specs");
Nmoltype = 0;
for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, ntypes);
for (i = 0; i < Nmoltype; i++) {
std::string molname;
for (j = 0; j < ntypes; j++) {
itemp = MolType[ntypes * i + j];
if (itemp != 0) {
if (eletype)
fprintf(fp, "%s", eletype[j]);
molname += eletype[j];
else
fprintf(fp, "%c", ele[j]);
if (itemp != 1) fprintf(fp, "%d", itemp);
molname += ele[j];
if (itemp != 1) molname += std::to_string(itemp);
}
}
fputs("\t", fp);
fmt::print(fp, " {:>11}", molname);
}
fputs("\n", fp);
fmt::print(fp, "{} {:11} {:11}\t", ntimestep, Nmole, Nspec);
for (i = 0; i < Nmoltype; i++) fprintf(fp, " %d\t", NMol[i]);
fprintf(fp, "\n");
fmt::print(fp, "{:>11} {:>11} {:>11}", ntimestep, Nmole, Nspec);
for (i = 0; i < Nmoltype; i++) fmt::print(fp, " {:>11}", NMol[i]);
fputs("\n", fp);
}
/* ---------------------------------------------------------------------- */
@ -884,8 +890,8 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
int ndeletions;
int headroom = -1;
if (delete_Nsteps > 0) {
if (delete_Tcount[delete_Nsteps-1] == -1) return;
ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps-1];
if (delete_Tcount[delete_Nsteps - 1] == -1) return;
ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps - 1];
if (delete_Nlimit_varid > -1)
delete_Nlimit = input->variable->compute_equal(delete_Nlimit_varid);
headroom = MAX(0, delete_Nlimit - ndeletions);
@ -925,13 +931,11 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
std::random_device rnd;
std::minstd_rand park_rng(rnd());
int *molrange;
memory->create(molrange,Nmole,"reaxff/species:molrange");
for (m = 0; m < Nmole; m++)
molrange[m] = m + 1;
memory->create(molrange, Nmole, "reaxff/species:molrange");
for (m = 0; m < Nmole; m++) molrange[m] = m + 1;
if (delete_Nsteps > 0) {
// shuffle index when using rate_limit, in case order is biased
if (comm->me == 0)
std::shuffle(&molrange[0],&molrange[Nmole], park_rng);
if (comm->me == 0) std::shuffle(&molrange[0], &molrange[Nmole], park_rng);
MPI_Bcast(&molrange[0], Nmole, MPI_INT, 0, world);
}
@ -1060,11 +1064,9 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
}
}
// push back delete_Tcount on every step
if (delete_Nsteps > 0) {
for (i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
for (i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
delete_Tcount[0] += this_delete_Tcount;
}

2
src/REAXFF/fix_reaxff_species.h
View File

@ -51,8 +51,6 @@ class FixReaxFFSpecies : public Fix {
int *Mol2Spec;
double *clusterID;
AtomCoord *x0;
double bg_cut;
double **BOCut;
std::vector<std::string> del_species;

279
src/library.cpp
View File

@ -247,6 +247,8 @@ void *lammps_open_no_mpi(int argc, char **argv, void **ptr)
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
This function is a version of :cpp:func:`lammps_open`, that uses an
integer for the MPI communicator as the MPI Fortran interface does. It
is used in the :f:func:`lammps` constructor of the LAMMPS Fortran
@ -257,8 +259,6 @@ communicator with ``MPI_Comm_f2c()`` and then calls
If for some reason the creation or initialization of the LAMMPS instance
fails a null pointer is returned.
.. versionadded:: 18Sep2020
*See also*
:cpp:func:`lammps_open_fortran`, :cpp:func:`lammps_open_no_mpi`
@ -304,13 +304,13 @@ void lammps_close(void *handle)
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
The MPI standard requires that any MPI application must call
``MPI_Init()`` exactly once before performing any other MPI function
calls. This function checks, whether MPI is already initialized and
calls ``MPI_Init()`` in case it is not.
.. versionadded:: 18Sep2020
\endverbatim */
void lammps_mpi_init()
@ -333,6 +333,8 @@ void lammps_mpi_init()
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
The MPI standard requires that any MPI application calls
``MPI_Finalize()`` before exiting. Even if a calling program does not
do any MPI calls, MPI is still initialized internally to avoid errors
@ -341,8 +343,6 @@ before exiting the program to wait until all (parallel) tasks are
completed and then MPI is cleanly shut down. After calling this
function no more MPI calls may be made.
.. versionadded:: 18Sep2020
*See also*
:cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_python_finalize`
\endverbatim */
@ -366,6 +366,8 @@ void lammps_mpi_finalize()
*
\verbatim embed:rst
.. versionadded:: 2Jul2021
The Kokkos library may only be initialized once during the execution of
a process. This is done automatically the first time Kokkos
functionality is used. This requires that the Kokkos environment
@ -373,8 +375,6 @@ must be explicitly shut down after any LAMMPS instance using it is
closed (to release associated resources).
After calling this function no Kokkos functionality may be used.
.. versionadded:: 2Jul2021
*See also*
:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_python_finalize`
\endverbatim */
@ -390,6 +390,8 @@ void lammps_kokkos_finalize()
*
\verbatim embed:rst
.. versionadded:: 20Sep2021
This function resets and clears an embedded Python environment
by calling the `Py_Finalize() function
<https://docs.python.org/3/c-api/init.html#c.Py_FinalizeEx>`_
@ -409,8 +411,6 @@ after calling Py_Finalize().
This function can be called to explicitly clear the Python
environment in case it is safe to do so.
.. versionadded:: 20Sep2021
*See also*
:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`
\endverbatim */
@ -427,6 +427,8 @@ void lammps_python_finalize()
*
\verbatim embed:rst
.. versionadded:: 3Nov2022
This function is a wrapper around functions in the ``Error`` to print an
error message and then stop LAMMPS.
@ -435,8 +437,6 @@ of constants from :cpp:enum:`_LMP_ERROR_CONST`. If the value does not
match any valid combination of constants a warning is printed and the
function returns.
.. versionadded:: 3Nov2022
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
@ -719,14 +719,16 @@ double lammps_get_natoms(void *handle)
/* ---------------------------------------------------------------------- */
/** Get current value of a thermo keyword.
/** Evaluate a thermo keyword.
*
\verbatim embed:rst
This function returns the current value of a :doc:`thermo keyword
<thermo_style>`. Unlike :cpp:func:`lammps_extract_global` it does not
give access to the storage of the desired data but returns its value as
a ``double``, so it can also return information that is computed on-the-fly.
This function returns the current value of a :doc:`thermo keyword <thermo_style>`.
Unlike :cpp:func:`lammps_extract_global` it does not give access to the
storage of the desired data but returns its value as a ``double``, so it
can also return information that is computed on-the-fly.
Use :cpp:func:`lammps_last_thermo` to get access to the cached data from
the last thermo output.
\endverbatim
*
@ -750,6 +752,117 @@ double lammps_get_thermo(void *handle, const char *keyword)
/* ---------------------------------------------------------------------- */
/** Access cached data from last thermo output
*
\verbatim embed:rst
.. versionadded:: TBD
This function provides access to cached data from the last thermo output.
This differs from :cpp:func:`lammps_get_thermo` in that it does not trigger
an evaluation. Instead it provides direct access to a read-only location
of the last thermo output data and the corresponding keyword strings.
The how to handle the return value depends on the value of the *what*
argument string.
.. note::
The *type* property points to a static location that is reassigned
with every call, so the returned pointer should be recast,
dereferenced, and assigned immediately. Otherwise, its value may be
changed with the next invocation of the function.
.. list-table::
:header-rows: 1
:widths: auto
* - Value of *what*
- Description of return value
- Data type
- Uses index
* - step
- timestep when the last thermo output was generated or -1
- pointer to bigint
- no
* - num
- number of fields in thermo output
- pointer to int
- no
* - keyword
- column keyword for thermo output
- pointer to 0-terminated const char array
- yes
* - type
- data type of thermo output column; see :cpp:enum:`_LMP_DATATYPE_CONST`
- pointer to static int
- yes
* - data
- actual field data for column
- pointer to int, int64_t or double
- yes
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param what string with the kind of data requested
* \param index integer with index into data arrays, ignored for scalar data
* \return pointer to location of requested data cast to void or NULL */
void *lammps_last_thermo(void *handle, const char *what, int index)
{
auto lmp = (LAMMPS *) handle;
void *val = nullptr;
Thermo *th = lmp->output->thermo;
if (!th) return nullptr;
const int nfield = *th->get_nfield();
static int datatype;
BEGIN_CAPTURE
{
if (strcmp(what, "step") == 0) {
val = (void *) th->get_timestep();
} else if (strcmp(what, "num") == 0) {
val = (void *) th->get_nfield();
} else if (strcmp(what, "keyword") == 0) {
if ((index < 0) || (index >= nfield)) return nullptr;
const auto &keywords = th->get_keywords();
val = (void *) keywords[index].c_str();
} else if (strcmp(what, "type") == 0) {
if ((index < 0) || (index >= nfield)) return nullptr;
const auto &field = th->get_fields()[index];
if (field.type == multitype::INT) {
datatype = LAMMPS_INT;
val = (void *) &datatype;
} else if (field.type == multitype::BIGINT) {
datatype = LAMMPS_INT64;
val = (void *) &datatype;
} else if (field.type == multitype::DOUBLE) {
datatype = LAMMPS_DOUBLE;
val = (void *) &datatype;
}
} else if (strcmp(what, "data") == 0) {
if ((index < 0) || (index >= nfield)) return nullptr;
const auto &field = th->get_fields()[index];
if (field.type == multitype::INT) {
val = (void *) &field.data.i;
} else if (field.type == multitype::BIGINT) {
val = (void *) &field.data.b;
} else if (field.type == multitype::DOUBLE) {
val = (void *) &field.data.d;
}
} else val = nullptr;
}
END_CAPTURE
return val;
}
/* ---------------------------------------------------------------------- */
/** Extract simulation box parameters.
*
\verbatim embed:rst
@ -877,6 +990,8 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
This function will retrieve memory usage information for the current
LAMMPS instance or process. The *meminfo* buffer will be filled with
3 different numbers (if supported by the operating system). The first
@ -889,8 +1004,6 @@ third number is the maximum amount of RAM (not swap) used by the process
so far. If any of the two latter parameters is not supported by the operating
system it will be set to zero.
.. versionadded:: 18Sep2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
@ -910,6 +1023,8 @@ void lammps_memory_usage(void *handle, double *meminfo)
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
This will take the LAMMPS "world" communicator and convert it to an
integer using ``MPI_Comm_c2f()``, so it is equivalent to the
corresponding MPI communicator in Fortran. This way it can be safely
@ -918,8 +1033,6 @@ to the C language representation use ``MPI_Comm_f2c()``.
If LAMMPS was compiled with MPI_STUBS, this function returns -1.
.. versionadded:: 18Sep2020
*See also*
:cpp:func:`lammps_open_fortran`
@ -1182,13 +1295,13 @@ int lammps_extract_setting(void *handle, const char *keyword)
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
This function returns an integer that encodes the data type of the global
property with the specified name. See :cpp:enum:`_LMP_DATATYPE_CONST` for valid
values. Callers of :cpp:func:`lammps_extract_global` can use this information
to then decide how to cast the ``void *`` pointer and access the data.
.. versionadded:: 18Sep2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance (unused)
@ -1671,13 +1784,13 @@ void *lammps_extract_global(void *handle, const char *name)
*
\verbatim embed:rst
.. versionadded:: 18Sep2020
This function returns an integer that encodes the data type of the per-atom
property with the specified name. See :cpp:enum:`_LMP_DATATYPE_CONST` for valid
values. Callers of :cpp:func:`lammps_extract_atom` can use this information
to then decide how to cast the ``void *`` pointer and access the data.
.. versionadded:: 18Sep2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
@ -2206,13 +2319,13 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
*
\verbatim embed:rst
.. versionadded:: 3Nov2022
This function returns an integer that encodes the data type of the variable
with the specified name. See :cpp:enum:`_LMP_VAR_CONST` for valid values.
Callers of :cpp:func:`lammps_extract_variable` can use this information to
decide how to cast the ``void *`` pointer and access the data.
.. versionadded:: 3Nov2022
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
@ -3064,6 +3177,8 @@ void lammps_scatter_atoms_subset(void *handle, const char *name, int type,
*
\verbatim embed:rst
.. versionadded:: 28Jul2021
This function copies the list of all bonds into a buffer provided by
the calling code. The buffer will be filled with bond type, bond atom 1,
bond atom 2 for each bond. Thus the buffer has to be allocated to the
@ -3078,8 +3193,6 @@ When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** bonds
in the system.
.. versionadded:: 28Jul2021
Below is a brief C code demonstrating accessing this collected bond information.
.. code-block:: c
@ -3159,7 +3272,8 @@ void lammps_gather_bonds(void *handle, void *data)
}
tagint **bonds;
lmp->memory->create(bonds, localbonds, 3, "library:gather_bonds:localbonds");
// add 1 to localbonds, so "bonds" does not become a NULL pointer
lmp->memory->create(bonds, localbonds+1, 3, "library:gather_bonds:localbonds");
lmp->atom->avec->pack_bond(bonds);
MPI_Allgatherv(&bonds[0][0], 3*localbonds, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
@ -3174,6 +3288,8 @@ void lammps_gather_bonds(void *handle, void *data)
*
\verbatim embed:rst
.. versionadded:: 8Feb2023
This function copies the list of all angles into a buffer provided by
the calling code. The buffer will be filled with angle type, angle atom 1,
angle atom 2, angle atom 3 for each angle. Thus the buffer has to be allocated to the
@ -3188,8 +3304,6 @@ When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** angles
in the system.
.. versionadded:: 8Feb2023
Below is a brief C code demonstrating accessing this collected angle information.
.. code-block:: c
@ -3269,7 +3383,8 @@ void lammps_gather_angles(void *handle, void *data)
}
tagint **angles;
lmp->memory->create(angles, localangles, 4, "library:gather_angles:localangles");
// add 1 to localangles, so "angles" does not become a NULL pointer
lmp->memory->create(angles, localangles+1, 4, "library:gather_angles:localangles");
lmp->atom->avec->pack_angle(angles);
MPI_Allgatherv(&angles[0][0], 4*localangles, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
@ -3284,6 +3399,8 @@ void lammps_gather_angles(void *handle, void *data)
*
\verbatim embed:rst
.. versionadded:: 8Feb2023
This function copies the list of all dihedrals into a buffer provided by
the calling code. The buffer will be filled with dihedral type, dihedral atom 1,
dihedral atom 2, dihedral atom 3, dihedral atom 4 for each dihedral.
@ -3299,8 +3416,6 @@ When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** dihedrals
in the system.
.. versionadded:: 8Feb2023
Below is a brief C code demonstrating accessing this collected dihedral information.
.. code-block:: c
@ -3380,7 +3495,8 @@ void lammps_gather_dihedrals(void *handle, void *data)
}
tagint **dihedrals;
lmp->memory->create(dihedrals, localdihedrals, 5, "library:gather_dihedrals:localdihedrals");
// add 1 to localdihedrals, so "dihedrals" does not become a NULL pointer
lmp->memory->create(dihedrals, localdihedrals+1, 5, "library:gather_dihedrals:localdihedrals");
lmp->atom->avec->pack_dihedral(dihedrals);
MPI_Allgatherv(&dihedrals[0][0], 5*localdihedrals, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
@ -3395,6 +3511,8 @@ void lammps_gather_dihedrals(void *handle, void *data)
*
\verbatim embed:rst
.. versionadded:: 8Feb2023
This function copies the list of all impropers into a buffer provided by
the calling code. The buffer will be filled with improper type, improper atom 1,
improper atom 2, improper atom 3, improper atom 4 for each improper.
@ -3410,8 +3528,6 @@ When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** impropers
in the system.
.. versionadded:: 8Feb2023
Below is a brief C code demonstrating accessing this collected improper information.
.. code-block:: c
@ -3491,7 +3607,8 @@ void lammps_gather_impropers(void *handle, void *data)
}
tagint **impropers;
lmp->memory->create(impropers, localimpropers, 5, "library:gather_impropers:localimpropers");
// add 1 to localimpropers, so "impropers" does not become a NULL pointer
lmp->memory->create(impropers, localimpropers+1, 5, "library:gather_impropers:localimpropers");
lmp->atom->avec->pack_improper(impropers);
MPI_Allgatherv(&impropers[0][0], 5*localimpropers, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
@ -5204,6 +5321,8 @@ int lammps_version(void *handle)
*
\verbatim embed:rst
.. versionadded:: 9Oct2020
The :cpp:func:`lammps_get_os_info` function can be used to retrieve
detailed information about the hosting operating system and
compiler/runtime.
@ -5212,8 +5331,6 @@ A suitable buffer for a C-style string has to be provided and its length.
The assembled text will be truncated to not overflow this buffer. The
string is typically a few hundred bytes long.
.. versionadded:: 9Oct2020
\endverbatim
*
* \param buffer string buffer to copy the information to
@ -5442,6 +5559,8 @@ int lammps_config_accelerator(const char *package,
*
\verbatim embed:rst
.. versionadded:: 14May2021
The :cpp:func:`lammps_has_gpu_device` function checks at runtime if
an accelerator device is present that can be used with the
:doc:`GPU package <Speed_gpu>`. If at least one suitable device is
@ -5451,8 +5570,6 @@ More detailed information about the available device or devices can
be obtained by calling the
:cpp:func:`lammps_get_gpu_device_info` function.
.. versionadded:: 14May2021
\endverbatim
*
* \return 1 if viable device is available, 0 if not. */
@ -5466,6 +5583,8 @@ int lammps_has_gpu_device()
*
\verbatim embed:rst
.. versionadded:: 14May2021
The :cpp:func:`lammps_get_gpu_device_info` function can be used to retrieve
detailed information about any accelerator devices that are viable for use
with the :doc:`GPU package <Speed_gpu>`. It will produce a string that is
@ -5477,8 +5596,6 @@ A suitable buffer for a C-style string has to be provided and its length.
The assembled text will be truncated to not overflow this buffer. This
string can be several kilobytes long, if multiple devices are present.
.. versionadded:: 14May2021
\endverbatim
*
* \param buffer string buffer to copy the information to
@ -5575,12 +5692,13 @@ int lammps_style_name(void *handle, const char *category, int idx,
/** Check if a specific ID exists in the current LAMMPS instance
*
\verbatim embed:rst
.. versionadded:: 9Oct2020
This function checks if the current LAMMPS instance a *category* ID of
the given *name* exists. Valid categories are: *compute*\ , *dump*\ ,
*fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ .
.. versionadded:: 9Oct2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5614,13 +5732,14 @@ int lammps_has_id(void *handle, const char *category, const char *name) {
/** Count the number of IDs of a category.
*
\verbatim embed:rst
.. versionadded:: 9Oct2020
This function counts how many IDs in the provided *category*
are defined in the current LAMMPS instance.
Please see :cpp:func:`lammps_has_id` for a list of valid
categories.
.. versionadded:: 9Oct2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5652,6 +5771,9 @@ int lammps_id_count(void *handle, const char *category) {
/** Look up the name of an ID by index in the list of IDs of a given category.
*
\verbatim embed:rst
.. versionadded:: 9Oct2020
This function copies the name of the *category* ID with the index
*idx* into the provided C-style string buffer. The length of the buffer
must be provided as *buf_size* argument. If the name of the style
@ -5659,8 +5781,6 @@ exceeds the length of the buffer, it will be truncated accordingly.
If the index is out of range, the function returns 0 and *buffer* is
set to an empty string, otherwise 1.
.. versionadded:: 9Oct2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5723,10 +5843,11 @@ int lammps_id_name(void *handle, const char *category, int idx, char *buffer, in
/** Count the number of loaded plugins
*
\verbatim embed:rst
This function counts how many plugins are currently loaded.
.. versionadded:: 10Mar2021
This function counts how many plugins are currently loaded.
\endverbatim
*
* \return number of loaded plugins
@ -5745,6 +5866,9 @@ int lammps_plugin_count()
/** Look up the info of a loaded plugin by its index in the list of plugins
*
\verbatim embed:rst
.. versionadded:: 10Mar2021
This function copies the name of the *style* plugin with the index
*idx* into the provided C-style string buffer. The length of the buffer
must be provided as *buf_size* argument. If the name of the style
@ -5752,8 +5876,6 @@ exceeds the length of the buffer, it will be truncated accordingly.
If the index is out of range, the function returns 0 and *buffer* is
set to an empty string, otherwise 1.
.. versionadded:: 10Mar2021
\endverbatim
*
* \param idx index of the plugin in the list all or *style* plugins
@ -5912,9 +6034,11 @@ void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalF
\verbatim embed:rst
Fix :doc:`external <fix_external>` allows programs that are running LAMMPS through
its library interface to add or modify certain LAMMPS properties on specific
timesteps, similar to the way other fixes do.
.. versionadded:: 28Jul2021
Fix :doc:`external <fix_external>` allows programs that are running
LAMMPS through its library interface to add or modify certain LAMMPS
properties on specific timesteps, similar to the way other fixes do.
This function provides access to the per-atom force storage in a fix
external instance with the given fix-ID to be added to the individual
@ -5927,12 +6051,12 @@ data structures can change as well as the order of atom as they migrate
between MPI processes because of the domain decomposition
parallelization, this function should be always called immediately
before the forces are going to be set to get an up-to-date pointer.
You can use, for example, :cpp:func:`lammps_extract_setting` to obtain the
number of local atoms `nlocal` and then assume the dimensions of the returned
force array as ``double force[nlocal][3]``.
You can use, for example, :cpp:func:`lammps_extract_setting` to obtain
the number of local atoms `nlocal` and then assume the dimensions of
the returned force array as ``double force[nlocal][3]``.
This is an alternative to the callback mechanism in fix external set up by
:cpp:func:`lammps_set_fix_external_callback`. The main difference is
This is an alternative to the callback mechanism in fix external set up
by :cpp:func:`lammps_set_fix_external_callback`. The main difference is
that this mechanism can be used when forces are be pre-computed and the
control alternates between LAMMPS and the external code, while the
callback mechanism can call the external code to compute the force when
@ -5942,8 +6066,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5974,6 +6096,8 @@ double **lammps_fix_external_get_force(void *handle, const char *id)
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
:cpp:func:`lammps_fix_external_get_force` to also set the contribution
to the global energy from the external code. The value of the *eng*
@ -5990,8 +6114,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6020,6 +6142,8 @@ void lammps_fix_external_set_energy_global(void *handle, const char *id, double
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
and :cpp:func:`lammps_fix_external_get_force` to set the contribution to
the global virial from the external code.
@ -6038,8 +6162,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6068,6 +6190,8 @@ void lammps_fix_external_set_virial_global(void *handle, const char *id, double
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
to set the per-atom energy contribution due to the fix from the external code
as part of the callback function. For this to work, the handle to the
@ -6086,8 +6210,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6116,6 +6238,8 @@ void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
to set the per-atom virial contribution due to the fix from the external code
as part of the callback function. For this to work, the handle to the
@ -6137,8 +6261,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6167,6 +6289,8 @@ void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
:cpp:func:`lammps_fix_external_get_force` to set the length of a global vector of
properties that will be stored with the fix via
@ -6181,8 +6305,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6211,6 +6333,8 @@ void lammps_fix_external_set_vector_length(void *handle, const char *id, int len
\verbatim embed:rst
.. versionadded:: 28Jul2021
This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
:cpp:func:`lammps_fix_external_get_force` to set the values of a global vector of
properties that will be stored with the fix. And can be accessed from
@ -6234,8 +6358,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -6407,12 +6529,13 @@ int lammps_get_last_error_message(void *handle, char *buffer, int buf_size) {
/** Return API version of embedded Python interpreter
\verbatim embed:rst
.. versionadded:: 3Nov2022
This function is used by the ML-IAP python code (mliappy) to verify
the API version of the embedded python interpreter of the PYTHON
package. It returns -1 if the PYTHON package is not enabled.
.. versionadded:: 3Nov2022
\endverbatim
*
* \return PYTHON_API_VERSION constant of the python interpreter or -1 */

1
src/library.h
View File

@ -148,6 +148,7 @@ void lammps_commands_string(void *handle, const char *str);
double lammps_get_natoms(void *handle);
double lammps_get_thermo(void *handle, const char *keyword);
void *lammps_last_thermo(void *handle, const char *what, int index);
void lammps_extract_box(void *handle, double *boxlo, double *boxhi, double *xy, double *yz,
double *xz, int *pflags, int *boxflag);

82
src/lmptype.h
View File

@ -95,7 +95,7 @@ typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT64_MAX
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_IMAGEINT MPI_INT
@ -133,7 +133,7 @@ typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT64_MAX
#define MAXBIGINT INT64_MAX
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MPI_LMP_TAGINT MPI_LL
#define MPI_LMP_IMAGEINT MPI_LL
@ -232,6 +232,84 @@ union ubuf {
ubuf(const int64_t &arg) : i(arg) {}
ubuf(const int &arg) : i(arg) {}
};
/** Data structure for dynamic typing of int, bigint, and double
*
* Using this union allows to store any of the supported data types
* in the same container and allows to "see" its current type.
\verbatim embed:rst
**Usage:**
.. code-block:: c++
:caption: To store data in multitype array:
multitype m[5];
int foo = 1;
double bar = 2.5;
bigint baz = 1<<40 - 1;
m[0] = foo;
m[1] = bar;
m[2] = -1;
m[3] = 2.0;
m[4] = baz;
.. code-block:: c++
:caption: To format data from multitype array into a space separated string:
std::string str;
for (int i = 0; i < 5; ++i) {
switch (m[i].type) {
case multitype::DOUBLE:
str += std::to_string(m[i].data.d) + ' ';
break;
case multitype::INT:
str += std::to_string(m[i].data.i) + ' ';
break;
case multitype::BIGINT:
str += std::to_string(m[i].data.b) + ' ';
break;
default:
break;
}
}
\endverbatim
*/
struct multitype {
enum { NONE, DOUBLE, INT, BIGINT };
int type;
union {
double d;
int i;
int64_t b;
} data;
multitype() : type(NONE) { data.d = 0.0; }
multitype(const multitype &) = default;
multitype(multitype &&) = default;
~multitype() = default;
multitype &operator=(const double &_d)
{
type = DOUBLE;
data.d = _d;
return *this;
}
multitype &operator=(const int &_i)
{
type = INT;
data.i = _i;
return *this;
}
multitype &operator=(const int64_t &_b)
{
type = BIGINT;
data.b = _b;
return *this;
}
};
} // namespace LAMMPS_NS
// preprocessor macros for compiler specific settings

3
src/my_page.h
View File

@ -104,6 +104,9 @@ template <class T> class MyPage {
int errorflag; // flag > 0 if error has occurred
// 1 = chunk size exceeded maxchunk
// 2 = memory allocation error
#if defined(_OPENMP)
char pad[64]; // to avoid false sharing with multi-threading
#endif
void allocate();
void deallocate();
};

108
src/output.cpp
View File

@ -190,6 +190,32 @@ void Output::setup(int memflag)
{
bigint ntimestep = update->ntimestep;
// print memory usage unless being called between multiple runs
if (memflag) memory_usage();
// set next_thermo to multiple of every or variable eval if var defined
// ensure thermo output on last step of run
// thermo may invoke computes so wrap with clear/add
modify->clearstep_compute();
thermo->header();
thermo->compute(0);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) {
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else next_thermo = update->laststep;
modify->addstep_compute(next_thermo);
// consider all dumps
// decide whether to write snapshot and/or calculate next step for dump
@ -257,7 +283,7 @@ void Output::setup(int memflag)
next_dump_any = MIN(next_dump_any,next_dump[idump]);
}
// if no dumps, set next_dump_any to last+1 so will not influence next
// if no dumps, set next_dump_any to last+1 so will not influence next
} else next_dump_any = update->laststep + 1;
@ -276,7 +302,8 @@ void Output::setup(int memflag)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
nextrestart, ntimestep);
next_restart_single = nextrestart;
}
} else next_restart_single = update->laststep + 1;
@ -289,39 +316,14 @@ void Output::setup(int memflag)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
nextrestart, ntimestep);
next_restart_double = nextrestart;
}
} else next_restart_double = update->laststep + 1;
next_restart = MIN(next_restart_single,next_restart_double);
} else next_restart = update->laststep + 1;
// print memory usage unless being called between multiple runs
if (memflag) memory_usage();
// set next_thermo to multiple of every or variable eval if var defined
// ensure thermo output on last step of run
// thermo may invoke computes so wrap with clear/add
modify->clearstep_compute();
thermo->header();
thermo->compute(0);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) {
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else next_thermo = update->laststep;
modify->addstep_compute(next_thermo);
// next = next timestep any output will be done
next = MIN(next_dump_any,next_restart);
@ -336,6 +338,24 @@ void Output::setup(int memflag)
void Output::write(bigint ntimestep)
{
// ensure next_thermo forces output on last step of run
// thermo may invoke computes so wrap with clear/add
if (next_thermo == ntimestep) {
modify->clearstep_compute();
if (last_thermo != ntimestep) thermo->compute(1);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) next_thermo += thermo_every;
else next_thermo = update->laststep;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
}
// perform dump if its next_dump = current ntimestep
// but not if it was already written on this step
// set next_dump and also next_time_dump for mode_dump = 1
@ -401,7 +421,8 @@ void Output::write(bigint ntimestep)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
nextrestart, ntimestep);
next_restart_single = nextrestart;
modify->addstep_compute(next_restart_single);
}
@ -424,7 +445,8 @@ void Output::write(bigint ntimestep)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
nextrestart, ntimestep);
next_restart_double = nextrestart;
modify->addstep_compute(next_restart_double);
}
@ -433,24 +455,6 @@ void Output::write(bigint ntimestep)
next_restart = MIN(next_restart_single,next_restart_double);
}
// ensure next_thermo forces output on last step of run
// thermo may invoke computes so wrap with clear/add
if (next_thermo == ntimestep) {
modify->clearstep_compute();
if (last_thermo != ntimestep) thermo->compute(1);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) next_thermo += thermo_every;
else next_thermo = update->laststep;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
}
// next = next timestep any output will be done
next = MIN(next_dump_any,next_restart);
@ -647,7 +651,8 @@ void Output::reset_timestep(bigint ntimestep)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart < ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
nextrestart, ntimestep);
update->ntimestep++;
next_restart_single = nextrestart;
modify->addstep_compute(next_restart_single);
@ -666,7 +671,8 @@ void Output::reset_timestep(bigint ntimestep)
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart < ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
nextrestart, ntimestep);
update->ntimestep++;
next_restart_double = nextrestart;
modify->addstep_compute(next_restart_double);

30
src/thermo.cpp
View File

@ -111,6 +111,7 @@ Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) :
lostflag = lostbond = Thermo::ERROR;
lostbefore = warnbefore = 0;
flushflag = 0;
ntimestep = -1;
// set style and corresponding lineflag
// custom style builds its own line of keywords, including wildcard expansion
@ -201,6 +202,8 @@ void Thermo::init()
ValueTokenizer *format_line = nullptr;
if (format_line_user.size()) format_line = new ValueTokenizer(format_line_user);
field_data.clear();
field_data.resize(nfield);
std::string format_this, format_line_user_def;
for (int i = 0; i < nfield; i++) {
@ -208,6 +211,14 @@ void Thermo::init()
format_this.clear();
format_line_user_def.clear();
if (vtype[i] == FLOAT) {
field_data[i] = (double) 0.0;
} else if (vtype[i] == INT) {
field_data[i] = (int) 0;
} else if (vtype[i] == BIGINT) {
field_data[i] = (bigint) 0;
}
if ((lineflag == MULTILINE) && ((i % 3) == 0)) format[i] += "\n";
if ((lineflag == YAMLLINE) && (i == 0)) format[i] += " - [";
if (format_line) format_line_user_def = format_line->next_string();
@ -361,7 +372,7 @@ void Thermo::compute(int flag)
int i;
firststep = flag;
bigint ntimestep = update->ntimestep;
ntimestep = update->ntimestep;
// check for lost atoms
// turn off normflag if natoms = 0 to avoid divide by 0
@ -405,18 +416,23 @@ void Thermo::compute(int flag)
}
// add each thermo value to line with its specific format
field_data.clear();
field_data.resize(nfield);
for (ifield = 0; ifield < nfield; ifield++) {
(this->*vfunc[ifield])();
if (vtype[ifield] == FLOAT) {
snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), dvalue);
line += fmtbuf;
field_data[ifield] = dvalue;
} else if (vtype[ifield] == INT) {
snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), ivalue);
line += fmtbuf;
field_data[ifield] = ivalue;
} else if (vtype[ifield] == BIGINT) {
snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), bivalue);
line += fmtbuf;
field_data[ifield] = bivalue;
}
}
@ -433,16 +449,6 @@ void Thermo::compute(int flag)
firststep = 1;
}
/* ----------------------------------------------------------------------
call function to compute property
------------------------------------------------------------------------- */
void Thermo::call_vfunc(int ifield_in)
{
ifield = ifield_in;
(this->*vfunc[ifield])();
}
/* ----------------------------------------------------------------------
check for lost atoms, return current number of atoms
also could number of warnings across MPI ranks and update total
@ -1062,6 +1068,8 @@ void Thermo::parse_fields(const std::string &str)
}
}
}
field_data.clear();
field_data.resize(nfield);
}
/* ----------------------------------------------------------------------

12
src/thermo.h
View File

@ -21,9 +21,6 @@ namespace LAMMPS_NS {
class Thermo : protected Pointers {
friend class MinCG; // accesses compute_pe
friend class DumpNetCDF; // accesses thermo properties
friend class DumpNetCDFMPIIO; // accesses thermo properties
friend class DumpYAML; // accesses thermo properties
public:
char *style;
@ -45,6 +42,12 @@ class Thermo : protected Pointers {
void compute(int);
int evaluate_keyword(const std::string &, double *);
// for accessing cached thermo data
const int *get_nfield() const { return &nfield; }
const bigint *get_timestep() const { return &ntimestep; }
const std::vector<multitype> &get_fields() const { return field_data; }
const std::vector<std::string> &get_keywords() const { return keyword; }
private:
int nfield, nfield_initial;
int *vtype;
@ -52,6 +55,7 @@ class Thermo : protected Pointers {
std::vector<std::string> keyword, format, format_column_user, keyword_user;
std::string format_line_user, format_float_user, format_int_user, format_bigint_user;
std::map<std::string, int> key2col;
std::vector<multitype> field_data;
int normvalue; // use this for normflag unless natoms = 0
int normuserflag; // 0 if user has not set, 1 if has
@ -66,6 +70,7 @@ class Thermo : protected Pointers {
bigint last_step;
bigint natoms;
bigint ntimestep;
// data used by routines that compute single values
int ivalue; // integer value to print
@ -114,7 +119,6 @@ class Thermo : protected Pointers {
typedef void (Thermo::*FnPtr)();
void addfield(const char *, FnPtr, int);
FnPtr *vfunc; // list of ptrs to functions
void call_vfunc(int ifield);
void compute_compute(); // functions that compute a single value
void compute_fix(); // via calls to Compute,Fix,Variable classes

4
src/variable.cpp
View File

@ -224,7 +224,7 @@ void Variable::set(int narg, char **arg)
if (narg == 5 && strcmp(arg[4],"pad") == 0) {
pad[nvar] = fmt::format("{}",nlast).size();
} else pad[nvar] = 0;
} else error->all(FLERR,"Illegal variable loop command: too much arguments");
} else error->all(FLERR,"Illegal variable loop command: too many arguments");
num[nvar] = nlast;
which[nvar] = nfirst-1;
data[nvar] = new char*[1];
@ -1052,7 +1052,7 @@ char *Variable::retrieve(const char *name)
if (vecs[ivar].dynamic || vecs[ivar].currentstep != update->ntimestep) {
eval_in_progress[ivar] = 0;
double *result;
int nvec = compute_vector(ivar,&result);
compute_vector(ivar,&result);
delete[] data[ivar][1];
std::vector <double> vectmp(vecs[ivar].values,vecs[ivar].values + vecs[ivar].n);
std::string str = fmt::format("[{}]", fmt::join(vectmp,","));

2
tools/coding_standard/versiontags.py
View File

@ -21,7 +21,7 @@ DEFAULT_CONFIG = """
recursive: true
include:
- doc/src/**
- python
- python/**
- src/**
exclude:
- src/Make.sh

2
tools/swig/lammps.i
View File

@ -113,6 +113,7 @@ extern void lammps_commands_string(void *handle, const char *str);
extern double lammps_get_natoms(void *handle);
extern double lammps_get_thermo(void *handle, const char *keyword);
extern void *lammps_last_thermo(void *handle, const char *what, int index);
extern void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
double *xy, double *yz, double *xz,
int *pflags, int *boxflag);
@ -295,6 +296,7 @@ extern void lammps_commands_string(void *handle, const char *str);
extern double lammps_get_natoms(void *handle);
extern double lammps_get_thermo(void *handle, const char *keyword);
extern void *lammps_last_thermo(void *handle, const char *what, int index);
extern void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
double *xy, double *yz, double *xz,
int *pflags, int *boxflag);

61
unittest/c-library/test_library_properties.cpp
View File

@ -14,6 +14,7 @@
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
using ::LAMMPS_NS::bigint;
using ::LAMMPS_NS::tagint;
using ::LAMMPS_NS::platform::path_join;
using ::testing::HasSubstr;
@ -93,6 +94,9 @@ TEST_F(LibraryProperties, natoms)
TEST_F(LibraryProperties, thermo)
{
bigint bval = *(bigint *)lammps_last_thermo(lmp, "step", 0);
EXPECT_EQ(bval, -1);
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = path_join(INPUT_DIR, "in.fourmol");
::testing::internal::CaptureStdout();
@ -105,6 +109,59 @@ TEST_F(LibraryProperties, thermo)
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3375.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "density"), 0.12211250945013695);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellalpha"), 90.0);
bval = *(bigint *)lammps_last_thermo(lmp, "step", 0);
EXPECT_EQ(bval, 2);
int ival = *(int *)lammps_last_thermo(lmp, "num", 0);
EXPECT_EQ(ival, 6);
const char *key = (const char *)lammps_last_thermo(lmp, "keyword", 0);
EXPECT_THAT(key, StrEq("Step"));
ival = *(int *)lammps_last_thermo(lmp, "type", 0);
#if defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(ival, LAMMPS_INT);
ival = *(int *)lammps_last_thermo(lmp, "data", 0);
EXPECT_EQ(ival, 2);
#else
EXPECT_EQ(ival, LAMMPS_INT64);
bval = *(bigint *)lammps_last_thermo(lmp, "data", 0);
EXPECT_EQ(bval, 2);
#endif
key = (const char *)lammps_last_thermo(lmp, "keyword", 1);
EXPECT_THAT(key, StrEq("Temp"));
ival = *(int *)lammps_last_thermo(lmp, "type", 1);
EXPECT_EQ(ival, LAMMPS_DOUBLE);
double dval = *(double *)lammps_last_thermo(lmp, "data", 1);
EXPECT_DOUBLE_EQ(dval, 28.042780385852982);
key = (const char *)lammps_last_thermo(lmp, "keyword", 2);
EXPECT_THAT(key, StrEq("E_pair"));
ival = *(int *)lammps_last_thermo(lmp, "type", 2);
EXPECT_EQ(ival, LAMMPS_DOUBLE);
dval = *(double *)lammps_last_thermo(lmp, "data", 2);
EXPECT_DOUBLE_EQ(dval, 0.0);
key = (const char *)lammps_last_thermo(lmp, "keyword", 3);
EXPECT_THAT(key, StrEq("E_mol"));
ival = *(int *)lammps_last_thermo(lmp, "type", 3);
EXPECT_EQ(ival, LAMMPS_DOUBLE);
dval = *(double *)lammps_last_thermo(lmp, "data", 3);
EXPECT_DOUBLE_EQ(dval, 0.0);
key = (const char *)lammps_last_thermo(lmp, "keyword", 4);
EXPECT_THAT(key, StrEq("TotEng"));
ival = *(int *)lammps_last_thermo(lmp, "type", 4);
EXPECT_EQ(ival, LAMMPS_DOUBLE);
dval = *(double *)lammps_last_thermo(lmp, "data", 4);
EXPECT_DOUBLE_EQ(dval, 2.3405256449146163);
key = (const char *)lammps_last_thermo(lmp, "keyword", 5);
EXPECT_THAT(key, StrEq("Press"));
ival = *(int *)lammps_last_thermo(lmp, "type", 5);
EXPECT_EQ(ival, LAMMPS_DOUBLE);
dval = *(double *)lammps_last_thermo(lmp, "data", 5);
EXPECT_DOUBLE_EQ(dval, 31.700964689115658);
};
TEST_F(LibraryProperties, box)
@ -325,8 +382,8 @@ TEST_F(LibraryProperties, global)
EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_lj"), LAMMPS_DOUBLE);
EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_coul"), LAMMPS_DOUBLE);
double *special_lj = (double *)lammps_extract_global(lmp, "special_lj");
double *special_coul= (double *)lammps_extract_global(lmp, "special_coul");
double *special_lj = (double *)lammps_extract_global(lmp, "special_lj");
double *special_coul = (double *)lammps_extract_global(lmp, "special_coul");
EXPECT_DOUBLE_EQ(special_lj[0], 1.0);
EXPECT_DOUBLE_EQ(special_lj[1], 0.0);
EXPECT_DOUBLE_EQ(special_lj[2], 0.5);

27
unittest/python/python-commands.py
View File

@ -533,6 +533,33 @@ create_atoms 1 single &
result = self.lmp.get_thermo(key)
self.assertEqual(value, result, key)
def test_last_thermo(self):
self.lmp.command("units lj")
self.lmp.command("atom_style atomic")
self.lmp.command("atom_modify map array")
self.lmp.command("boundary f f f")
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
self.lmp.command("mass * 1")
x = [
0.5, 0.5, 0.5,
1.5, 1.5, 1.5
]
types = [1, 1]
self.lmp.create_atoms(2, id=None, type=types, x=x)
self.assertEqual(self.lmp.last_thermo(), None)
self.lmp.command("run 2 post no")
ref = { "Step" : 2,
"Temp" : 0.0,
"E_pair" : 0.0,
"E_mol" : 0.0,
"TotEng" : 0.0,
"Press" : 0.0}
self.assertDictEqual(self.lmp.last_thermo(), ref)
def test_extract_global(self):
self.lmp.command("region box block -1 1 -2 2 -3 3")
self.lmp.command("create_box 1 box")

4
unittest/utils/CMakeLists.txt
View File

@ -7,6 +7,10 @@ add_executable(test_mempool test_mempool.cpp)
target_link_libraries(test_mempool PRIVATE lammps GTest::GMockMain)
add_test(NAME MemPool COMMAND test_mempool)
add_executable(test_lmptype test_lmptype.cpp)
target_link_libraries(test_lmptype PRIVATE lammps GTest::GMockMain)
add_test(NAME LmpType COMMAND test_lmptype)
add_executable(test_argutils test_argutils.cpp)
target_link_libraries(test_argutils PRIVATE lammps GTest::GMockMain)
add_test(NAME ArgUtils COMMAND test_argutils)

79
unittest/utils/test_lmptype.cpp Normal file
View File

@ -0,0 +1,79 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS Development team: developers@lammps.org
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 "lmptype.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <string>
using namespace LAMMPS_NS;
TEST(Types, ubuf)
{
double buf[3];
double d1 = 0.1;
int i1 = -10;
#if defined(LAMMPS_SMALLSMALL)
bigint b1 = 2048;
#else
bigint b1 = (1L << 58) + (1L << 50);
#endif
buf[0] = d1;
buf[1] = ubuf(i1).d;
buf[2] = ubuf(b1).d;
EXPECT_EQ(d1, buf[0]);
EXPECT_EQ(i1, (int)ubuf(buf[1]).i);
EXPECT_EQ(b1, (bigint)ubuf(buf[2]).i);
}
TEST(Types, multitype)
{
multitype m[7];
int64_t b1 = (3L << 48) - 1;
int i1 = 20;
double d1 = 0.1;
m[0] = b1;
m[1] = i1;
m[2] = d1;
m[3] = (bigint) -((1L << 40) + (1L << 50));
m[4] = -1023;
m[5] = -2.225;
EXPECT_EQ(m[0].type, multitype::BIGINT);
EXPECT_EQ(m[1].type, multitype::INT);
EXPECT_EQ(m[2].type, multitype::DOUBLE);
#if defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(m[3].type, multitype::INT);
#else
EXPECT_EQ(m[3].type, multitype::BIGINT);
#endif
EXPECT_EQ(m[4].type, multitype::INT);
EXPECT_EQ(m[5].type, multitype::DOUBLE);
EXPECT_EQ(m[6].type, multitype::NONE);
EXPECT_EQ(m[0].data.b, b1);
EXPECT_EQ(m[1].data.i, i1);
EXPECT_EQ(m[2].data.d, d1);
#if !defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(m[3].data.b, -((1L << 40) + (1L << 50)));
#endif
EXPECT_EQ(m[4].data.i, -1023);
EXPECT_EQ(m[5].data.d, -2.225);
}