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Merge pull request #3470 from hammondkd/fortran-further-tinkering

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Further extending the Fortran interface
This commit is contained in:
Axel Kohlmeyer
2022-10-05 21:20:06 -04:00
committed by GitHub
parent 7157643fdd 3a4d4b0756
commit 967c84cb69
50 changed files with 5394 additions and 917 deletions
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2
doc/src/Build_manual.rst
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@ -216,7 +216,7 @@ be multiple tests run automatically:
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like greek letters
prepended to the screen. Special characters like Greek letters
(:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
(:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
(:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol

1175
doc/src/Fortran.rst
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File diff suppressed because it is too large Load Diff

8
doc/src/Library_objects.rst
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@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_compute`
- :cpp:func:`lammps_extract_fix`
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
@ -21,6 +22,11 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_extract_variable_datatype
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_variable
:project: progguide
@ -36,3 +42,5 @@ fixes, or variables in LAMMPS using the following functions:
.. doxygenenum:: _LMP_STYLE_CONST
.. doxygenenum:: _LMP_TYPE_CONST
.. doxygenenum:: _LMP_VAR_CONST

10
doc/src/Library_properties.rst
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@ -16,8 +16,8 @@ This section documents the following functions:
--------------------
The library interface allows the extraction of different kinds of
information about the active simulation instance and also - in some
cases - to apply modifications to it. This enables combining of a
information about the active simulation instance and also---in some
cases---to apply modifications to it. This enables combining of a
LAMMPS simulation with other processing and simulation methods computed
by the calling code, or by another code that is coupled to LAMMPS via
the library interface. In some cases the data returned is direct
@ -25,9 +25,9 @@ reference to the original data inside LAMMPS, cast to a void pointer.
In that case the data needs to be cast to a suitable pointer for the
calling program to access it, and you may need to know the correct
dimensions and lengths. This also means you can directly change those
value(s) from the calling program, e.g. to modify atom positions. Of
course, this should be done with care. When accessing per-atom data,
please note that this data is the per-processor **local** data and is
value(s) from the calling program (e.g., to modify atom positions). Of
course, changing values should be done with care. When accessing per-atom
data, please note that these data are the per-processor **local** data and are
indexed accordingly. Per-atom data can change sizes and ordering at
every neighbor list rebuild or atom sort event as atoms migrate between
sub-domains and processors.

9
doc/src/Run_basics.rst
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@ -30,12 +30,13 @@ executable itself can be placed elsewhere.
.. note::
The redirection operator "<" will not always work when running
in parallel with mpirun or mpiexec; for those systems the -in form is required.
The redirection operator "<" will not always work when running in
parallel with ``mpirun`` or ``mpiexec``; for those systems the -in
form is required.
As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the
:doc:`screen and logfile output <Run_output>` page.
*log.lammps*\ . More info about output is given on the :doc:`screen and
logfile output <Run_output>` page.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING

20
doc/src/Run_options.rst
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@ -93,13 +93,13 @@ switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or OPENMP packages, for testing or benchmarking purposes.
Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
"mpirun" or "mpiexec" command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.
Additional optional keyword/value pairs can be specified which determine
how Kokkos will use the underlying hardware on your platform. These
settings apply to each MPI task you launch via the ``mpirun`` or
``mpiexec`` command. You may choose to run one or more MPI tasks per
physical node. Note that if you are running on a desktop machine, you
typically have one physical node. On a cluster or supercomputer there
may be dozens or 1000s of physical nodes.
Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
@ -148,9 +148,9 @@ one of these 4 environment variables
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
which are initialized by the ``srun``, ``mpirun``, or ``mpiexec``
commands. The environment variable setting for each MPI rank is used to
assign a unique GPU ID to the MPI task.
.. parsed-literal::

13
doc/src/Speed_gpu.rst
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@ -76,10 +76,11 @@ instructions.
**Run with the GPU package from the command line:**
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the ``mpirun`` command in MPICH does this via
its ``-np`` and ``-ppn`` switches. Ditto for OpenMPI via ``-np`` and
``-npernode``.
When using the GPU package, you cannot assign more than one GPU to a
single MPI task. However multiple MPI tasks can share the same GPU,
@ -129,8 +130,8 @@ GPU package pair styles.
**Or run with the GPU package by editing an input script:**
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and use of multiple MPI tasks/GPU is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and use of multiple MPI tasks/GPU is the same.
Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
"gpu" suffix to individual styles in your input script, e.g.

17
doc/src/Speed_kokkos.rst
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@ -72,12 +72,12 @@ See the :ref:`Build extras <kokkos>` page for instructions.
Running LAMMPS with the KOKKOS package
""""""""""""""""""""""""""""""""""""""
All Kokkos operations occur within the context of an individual MPI
task running on a single node of the machine. The total number of MPI
tasks used by LAMMPS (one or multiple per compute node) is set in the
usual manner via the mpirun or mpiexec commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
-npernode switches. Ditto for MPICH via -np and -ppn.
All Kokkos operations occur within the context of an individual MPI task
running on a single node of the machine. The total number of MPI tasks
used by LAMMPS (one or multiple per compute node) is set in the usual
manner via the ``mpirun`` or ``mpiexec`` commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its ``-np`` and
``-npernode`` switches. Ditto for MPICH via ``-np`` and ``-ppn``.
Running on a multi-core CPU
^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -168,7 +168,7 @@ for your MPI installation), binding can be forced with these flags:
.. parsed-literal::
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
For binding threads with KOKKOS OpenMP, use thread affinity environment
@ -310,7 +310,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
``mpirun`` or ``mpiexec`` command, and setting appropriate thread
properties are the same.
You must still use the "-k on" :doc:`command-line switch <Run_options>`
to enable the KOKKOS package, and specify its additional arguments for

8
doc/src/Speed_omp.rst
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@ -33,8 +33,8 @@ These examples assume one or more 16-core nodes.
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
@ -58,8 +58,8 @@ OMP_NUM_THREADS environment variable.
Or run with the OPENMP package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and threads/MPI task is the same.
Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.

5
doc/utils/sphinx-config/false_positives.txt
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@ -78,6 +78,7 @@ Alexey
ali
aliceblue
Allinger
allocatable
allocator
allocators
allosws
@ -657,6 +658,7 @@ Dcut
de
dE
De
deallocate
deallocated
debye
Debye
@ -691,6 +693,7 @@ dequidt
Dequidt
der
dereference
dereferenced
derekt
Deresiewicz
Derjagin
@ -1486,6 +1489,7 @@ interfacial
interial
interlayer
intermolecular
interoperable
Interparticle
interstitials
intertube
@ -3621,6 +3625,7 @@ Universite
unix
unmaintained
unoptimized
unordered
unpadded
unphysical
unphysically

8
fortran/README
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@ -1,9 +1,9 @@
This directory contains Fortran code which interface LAMMPS as a library
and allows the LAMMPS library interface to be invoked from Fortran codes.
It requires a Fortran compiler that supports the Fortran 2003 standard.
This directory contains Fortran code that acts as an interface to LAMMPS as a
library and allows the LAMMPS library interface to be invoked from Fortran
code. It requires a Fortran compiler that supports the Fortran 2003 standard.
This interface is based on and supersedes the previous Fortran interfaces
in the examples/COUPLE/fortran* folders, but is fully supported by the
in the examples/COUPLE/fortran* folders, but it is fully supported by the
LAMMPS developers and included in the documentation and unit testing.
Details on this Fortran interface and how to build programs using it

1515
fortran/lammps.f90
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File diff suppressed because it is too large Load Diff

4
python/examples/mc.py
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@ -60,7 +60,7 @@ lmp.command("thermo_style custom step v_emin v_elast pe")
lmp.command("run 0")
x = lmp.extract_atom("x")
lmp.command("variable elast equal $e")
estart = lmp.extract_compute("thermo_pe", LMP_STYLE_GLOBAL, LAMMPS_INT) / natoms
# loop over Monte Carlo moves
@ -92,7 +92,7 @@ for i in range(nloop):
else:
x[iatom][0] = x0
x[iatom][1] = y0
# final energy and stats
lmp.command("variable nbuild equal nbuild")

144
python/examples/pizza/gl.py
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@ -3,7 +3,7 @@
#
# Copyright (2005) 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
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
@ -19,8 +19,8 @@ g = gl(d) create OpenGL display for data in d
d = atom snapshot object (dump, data)
g.bg("black") set background color (def = "black")
g.size(N) set image size to NxN
g.size(N,M) set image size to NxM
g.size(N) set image size to NxN
g.size(N,M) set image size to NxM
g.rotate(60,135) view from z theta and azimuthal phi (def = 60,30)
g.shift(x,y) translate by x,y pixels in view window (def = 0,0)
g.zoom(0.5) scale image by factor (def = 1)
@ -30,7 +30,7 @@ g.box(0/1/2,"red",4) set box edge thickness
g.file = "image" file prefix for created images (def = "image")
g.show(N) show image of snapshot at timestep N
g.all() make images of all selected snapshots
g.all(P) images of all, start file label at P
g.all(N,M,P) make M images of snapshot N, start label at P
@ -43,12 +43,12 @@ g.pan() no pan during all() (default)
g.select = "$x > %g*3.0" string to pass to d.aselect.test() during all()
g.select = "" no extra aselect (default)
%g varies from 0.0 to 1.0 from beginning to end of all()
g.acol(2,"green") set atom colors by atom type (1-N)
g.acol([2,4],["red","blue"]) 1st arg = one type or list of types
g.acol(0,"blue") 2nd arg = one color or list of colors
g.acol(2,"green") set atom colors by atom type (1-N)
g.acol([2,4],["red","blue"]) 1st arg = one type or list of types
g.acol(0,"blue") 2nd arg = one color or list of colors
g.acol(range(20),["red","blue"]) if list lengths unequal, interpolate
g.acol(range(10),"loop") assign colors in loop, randomly ordered
@ -58,23 +58,23 @@ g.acol(range(10),"loop") assign colors in loop, randomly ordered
g.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol()
g.bcol() set bond color, same args as acol()
g.brad() set bond thickness, same args as arad()
g.bcol() set bond color, same args as acol()
g.brad() set bond thickness, same args as arad()
g.tcol() set triangle color, same args as acol()
g.tfill() set triangle fill, 0 fill, 1 line, 2 both
g.tcol() set triangle color, same args as acol()
g.tfill() set triangle fill, 0 fill, 1 line, 2 both
g.lcol() set line color, same args as acol()
g.lrad() set line thickness, same args as arad()
g.adef() set atom/bond/tri/line properties to default
g.bdef() default = "loop" for colors, 0.45 for radii
g.tdef() default = 0.25 for bond/line thickness
g.ldef() default = 0 fill
g.bdef() default = "loop" for colors, 0.45 for radii
g.tdef() default = 0.25 for bond/line thickness
g.ldef() default = 0 fill
by default 100 types are assigned
if atom/bond/tri/line has type > # defined properties, is an error
from vizinfo import colors access color list
print(colors) list defined color names and RGB values
colors["nickname"] = [R,G,B] set new RGB values from 0 to 255
@ -148,7 +148,7 @@ class gl:
self.azphi = 30
self.scale = 1.0
self.xshift = self.yshift = 0
self.file = "image"
self.boxflag = 0
self.bxcol = [1,1,0]
@ -165,7 +165,7 @@ class gl:
self.nsides = 10
self.theta_amplify = 2
self.shiny = 2
self.clipflag = 0
self.clipxlo = self.clipylo = self.clipzlo = 0.0
self.clipxhi = self.clipyhi = self.clipzhi = 1.0
@ -189,7 +189,7 @@ class gl:
self.bdef()
self.tdef()
self.ldef()
self.center = 3*[0]
self.view = 3*[0]
self.up = 3*[0]
@ -211,7 +211,7 @@ class gl:
if not ynew: self.ypixels = self.xpixels
else: self.ypixels = ynew
self.create_window()
# --------------------------------------------------------------------
def axis(self,value):
@ -223,7 +223,7 @@ class gl:
def create_window(self):
if self.root: self.root.destroy()
from __main__ import tkroot
self.root = Toplevel(tkroot)
self.root.title('Pizza.py gl tool')
@ -232,7 +232,7 @@ class gl:
double=1,depth=1)
self.w.pack(expand=YES)
# self.w.pack(expand=YES,fill=BOTH)
glViewport(0,0,self.xpixels,self.ypixels)
glEnable(GL_LIGHTING);
glEnable(GL_LIGHT0);
@ -247,7 +247,7 @@ class gl:
self.w.parent = self
self.w.tkRedraw()
tkroot.update_idletasks() # force window to appear
# --------------------------------------------------------------------
def clip(self,which,value):
@ -314,7 +314,7 @@ class gl:
self.up[1] = sin(pi*self.azphi/180)
self.up[2] = 0.0
else:
dot = self.view[2] # dot = (0,0,1) . view
dot = self.view[2] # dot = (0,0,1) . view
self.up[0] = -dot*self.view[0] # up projected onto v = dot * v
self.up[1] = -dot*self.view[1] # up perp to v = up - dot * v
self.up[2] = 1.0 - dot*self.view[2]
@ -325,7 +325,7 @@ class gl:
# --------------------------------------------------------------------
# reset ztheta,azphi and thus view,up.right
# called as function from Pizza.py
def rotate(self,ztheta,azphi):
self.ztheta = ztheta
self.azphi = azphi
@ -366,11 +366,11 @@ class gl:
# rotate view,up around axis of rotation = old x new
# right = up x view
# reset ztheta,azphi from view
def mouse_rotate(self,xnew,ynew,xold,yold):
# change y pixels to measure from bottom of window instead of top
yold = self.ypixels - yold
ynew = self.ypixels - ynew
@ -407,7 +407,7 @@ class gl:
axis[1] = rot[0]*self.right[1] + rot[1]*self.up[1] + rot[2]*self.view[1]
axis[2] = rot[0]*self.right[2] + rot[1]*self.up[2] + rot[2]*self.view[2]
axis = vecnorm(axis)
# view is changed by (axis x view) scaled by theta
# up is changed by (axis x up) scaled by theta
# force up to be perp to view via up_perp = up - (up . view) view
@ -468,14 +468,14 @@ class gl:
# output: eye = distance to view scene from
# xto,yto,zto = point to look to
# xfrom,yfrom,zfrom = point to look from
def setview(self):
if not self.ready: return # no distance since no scene yet
self.eye = 3 * self.distance / self.scale
xfactor = 0.5*self.eye*self.xshift/self.xpixels
yfactor = 0.5*self.eye*self.yshift/self.ypixels
self.xto = self.center[0] - xfactor*self.right[0] - yfactor*self.up[0]
self.yto = self.center[1] - xfactor*self.right[1] - yfactor*self.up[1]
self.zto = self.center[2] - xfactor*self.right[2] - yfactor*self.up[2]
@ -486,7 +486,7 @@ class gl:
# --------------------------------------------------------------------
# box attributes, also used for triangle lines
def box(self,*args):
self.boxflag = args[0]
if len(args) > 1:
@ -500,7 +500,7 @@ class gl:
# --------------------------------------------------------------------
# grab all selected snapshots from data object
# add GL-specific info to each bond
def reload(self):
print("Loading data into gl tool ...")
data = self.data
@ -529,7 +529,7 @@ class gl:
self.bondframes.append(bonds)
self.triframes.append(tris)
self.lineframes.append(lines)
print(time,end='')
sys.stdout.flush()
print()
@ -545,11 +545,11 @@ class gl:
def nolabel(self):
self.cachelist = -self.cachelist
self.labels = []
# --------------------------------------------------------------------
# show a single snapshot
# distance from snapshot box or max box for all selected steps
def show(self,ntime):
data = self.data
which = data.findtime(ntime)
@ -571,7 +571,7 @@ class gl:
self.cachelist = -self.cachelist
self.w.tkRedraw()
self.save()
# --------------------------------------------------------------------
def pan(self,*list):
@ -584,7 +584,7 @@ class gl:
self.ztheta_stop = list[3]
self.azphi_stop = list[4]
self.scale_stop = list[5]
# --------------------------------------------------------------------
def all(self,*list):
@ -615,7 +615,7 @@ class gl:
if flag == -1: break
fraction = float(i) / (ncount-1)
if self.select != "":
newstr = self.select % fraction
data.aselect.test(newstr,time)
@ -653,7 +653,7 @@ class gl:
self.cachelist = -self.cachelist
self.w.tkRedraw()
self.save(file)
print(time,end='')
sys.stdout.flush()
i += 1
@ -731,19 +731,19 @@ class gl:
# --------------------------------------------------------------------
# draw the GL scene
def redraw(self,o):
# clear window to background color
glClearColor(self.bgcol[0],self.bgcol[1],self.bgcol[2],0)
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
# not ready if no scene yet
if not self.ready: return
# set view from eye, distance, 3 lookat vectors (from,to,up)
glMatrixMode(GL_PROJECTION)
glLoadIdentity()
if self.orthoflag:
@ -759,14 +759,14 @@ class gl:
# draw scene from display list if caching allowed and list hasn't changed
# else redraw and store as new display list if caching allowed
if self.cache and self.cachelist > 0: glCallList(self.cachelist);
else:
if self.cache:
if self.cachelist < 0: glDeleteLists(-self.cachelist,1)
self.cachelist = glGenLists(1)
glNewList(self.cachelist,GL_COMPILE_AND_EXECUTE)
# draw box, clip-box, xyz axes, lines
glDisable(GL_LIGHTING)
@ -842,7 +842,7 @@ class gl:
if self.tridraw:
fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])]
if fillflag != 1:
if fillflag:
glEnable(GL_POLYGON_OFFSET_FILL)
@ -921,7 +921,7 @@ class gl:
gluCylinder(obj,rad,rad,bond[10],self.nsides,self.nsides)
glPopMatrix()
if self.tridraw:
if self.tridraw:
fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])]
if fillflag != 1:
@ -975,7 +975,7 @@ class gl:
glEnd()
glEnable(GL_LIGHTING)
glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
if self.cache: glEndList()
glFlush()
@ -983,16 +983,16 @@ class gl:
# --------------------------------------------------------------------
# make new call list for each atom type
# called when atom color/rad/quality is changed
def make_atom_calllist(self):
# extend calllist array if necessary
if self.vizinfo.nacolor > self.nclist:
for i in range(self.vizinfo.nacolor-self.nclist): self.calllist.append(0)
self.nclist = self.vizinfo.nacolor
# create new calllist for each atom type
for itype in xrange(1,self.vizinfo.nacolor+1):
if self.calllist[itype]: glDeleteLists(self.calllist[itype],1)
ilist = glGenLists(1)
@ -1001,12 +1001,12 @@ class gl:
red,green,blue = self.vizinfo.acolor[itype]
rad = self.vizinfo.arad[itype]
glColor3f(red,green,blue);
# glPointSize(10.0*rad)
# glBegin(GL_POINTS)
# glVertex3f(0.0,0.0,0.0)
# glEnd()
glMaterialfv(GL_FRONT,GL_EMISSION,[red,green,blue,1.0]);
glMaterialf(GL_FRONT,GL_SHININESS,self.shiny);
glutSolidSphere(rad,self.nslices,self.nstacks)
@ -1015,7 +1015,7 @@ class gl:
# --------------------------------------------------------------------
# augment bond info returned by viz() with info needed for GL draw
# info = length, theta, -dy, dx for bond orientation
def bonds_augment(self,bonds):
for bond in bonds:
dx = bond[5] - bond[2]
@ -1046,7 +1046,7 @@ class gl:
glLineWidth(self.bxthick)
glColor3f(self.bxcol[0],self.bxcol[1],self.bxcol[2])
glBegin(GL_LINE_LOOP)
glVertex3f(xlo,ylo,zlo)
glVertex3f(xhi,ylo,zlo)
@ -1081,7 +1081,7 @@ class gl:
if yhi-ylo > delta: delta = yhi-ylo
if zhi-zlo > delta: delta = zhi-zlo
delta *= 0.1
glLineWidth(self.bxthick)
glBegin(GL_LINES)
@ -1100,7 +1100,7 @@ class gl:
def save(self,file=None):
self.w.update() # force image on screen to be current before saving it
pstring = glReadPixels(0,0,self.xpixels,self.ypixels,
GL_RGBA,GL_UNSIGNED_BYTE)
snapshot = Image.fromstring("RGBA",(self.xpixels,self.ypixels),pstring)
@ -1110,14 +1110,14 @@ class gl:
snapshot.save(file + ".png")
# --------------------------------------------------------------------
def adef(self):
self.vizinfo.setcolors("atom",range(100),"loop")
self.vizinfo.setradii("atom",range(100),0.45)
self.make_atom_calllist()
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def bdef(self):
@ -1130,14 +1130,14 @@ class gl:
def tdef(self):
self.vizinfo.setcolors("tri",range(100),"loop")
self.vizinfo.setfills("tri",range(100),0)
self.vizinfo.setfills("tri",range(100),0)
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def ldef(self):
self.vizinfo.setcolors("line",range(100),"loop")
self.vizinfo.setcolors("line",range(100),"loop")
self.vizinfo.setradii("line",range(100),0.25)
self.cachelist = -self.cachelist
self.w.tkRedraw()
@ -1149,29 +1149,29 @@ class gl:
self.make_atom_calllist()
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def arad(self,atypes,radii):
self.vizinfo.setradii("atom",atypes,radii)
self.vizinfo.setradii("atom",atypes,radii)
self.make_atom_calllist()
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def bcol(self,btypes,colors):
self.vizinfo.setcolors("bond",btypes,colors)
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def brad(self,btypes,radii):
self.vizinfo.setradii("bond",btypes,radii)
self.cachelist = -self.cachelist
self.w.tkRedraw()
# --------------------------------------------------------------------
def tcol(self,ttypes,colors):
@ -1210,10 +1210,10 @@ class MyOpengl(Opengl):
args = (self,master,cnf)
Opengl.__init__(*args,**kw)
Opengl.autospin_allowed = 0
# redraw Opengl scene
# call parent redraw() method
def tkRedraw(self,*dummy):
if not self.initialised: return
self.tk.call(self._w,'makecurrent')
@ -1222,7 +1222,7 @@ class MyOpengl(Opengl):
# left button translate
# access parent xshift/yshift and call parent trans() method
def tkTranslate(self,event):
dx = event.x - self.xmouse
dy = event.y - self.ymouse
@ -1242,7 +1242,7 @@ class MyOpengl(Opengl):
# right button zoom
# access parent scale and call parent zoom() method
def tkScale(self,event):
scale = 1 - 0.01 * (event.y - self.ymouse)
if scale < 0.001: scale = 0.001

28
python/examples/pizza/vizinfo.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) 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
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# vizinfo class, not a top-level Pizza.py tool
@ -25,7 +25,7 @@ import types
class vizinfo:
"""
Information holder for Pizza.py visualization tools
acolor,bcolor,tcolor,lcolor = RGB values for each atom/bond/tri/line type
arad = radius of each atom type
brad,lrad = thickness of each bond/line type
@ -41,7 +41,7 @@ class vizinfo:
setfill() = set triangle fill factor
extend() = grow an array
"""
# --------------------------------------------------------------------
def __init__(self):
@ -57,15 +57,15 @@ class vizinfo:
self.nbcolor = self.nbrad = 0
self.ntcolor = self.ntfill = 0
self.nlcolor = self.nlrad = 0
# --------------------------------------------------------------------
# set color RGB for which = atoms, bonds, triangles
def setcolors(self,which,ids,rgbs):
# convert args into lists if single values
# if arg = 0, convert to full-range list
if type(ids) is types.IntType and ids == 0:
if which == "atom": ids = range(self.nacolor)
if which == "bond": ids = range(self.nbcolor)
@ -101,11 +101,11 @@ class vizinfo:
if max(ids) > self.nlcolor:
self.nlcolor = self.extend(self.lcolor,max(ids))
self.nlcolor = self.extend(self.lrad,max(ids))
# set color for each type
# if list lengths match, set directly, else interpolate
# convert final color from 0-255 to 0.0-1.0
ntypes = len(ids)
nrgbs = len(rgbs)
@ -135,7 +135,7 @@ class vizinfo:
if which == "bond": self.bcolor[id] = color
if which == "tri": self.tcolor[id] = color
if which == "line": self.lcolor[id] = color
# --------------------------------------------------------------------
# set radii for which = atoms, bonds, lines
@ -143,7 +143,7 @@ class vizinfo:
# convert args into lists if single values
# if arg = 0, convert to full-range list
if type(ids) is types.IntType and ids == 0:
if which == "atom": ids = range(self.narad)
if which == "bond": ids = range(self.nbrad)
@ -199,16 +199,16 @@ class vizinfo:
if which == "atom": self.arad[id] = rad
if which == "bond": self.brad[id] = rad
if which == "line": self.lrad[id] = rad
# --------------------------------------------------------------------
# set triangle fill style
# 0 = fill only, 1 = line only, 2 = fill and line
def setfills(self,which,ids,fills):
# convert args into lists if single values
# if arg = 0, convert to full-range list
if type(ids) is types.IntType and ids == 0:
ids = range(self.ntfill)
if type(ids) is not types.ListType and type(ids) is not types.TupleType:
@ -237,7 +237,7 @@ class vizinfo:
for i in range(len(ids)): self.tfill[ids[i]] = int(fills[i])
else:
for id in ids: self.tfill[id] = int(fills[0])
# --------------------------------------------------------------------
def extend(self,array,n):

40
python/examples/pizza/vmd.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) 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
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
@ -20,24 +20,24 @@ from __future__ import print_function
oneline = "Control VMD from python"
docstr = """
v = vmd() start up VMD
v.stop() shut down VMD instance
v.clear() delete all visualizations
v = vmd() start up VMD
v.stop() shut down VMD instance
v.clear() delete all visualizations
v.rep(style) set default representation style. One of
(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
v.new(file[,type]) load new file (default file type 'lammpstrj')
v.rep(style) set default representation style. One of
(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
v.new(file[,type]) load new file (default file type 'lammpstrj')
v.data(file[,atomstyle]) load new data file (default atom style 'full')
v.replace(file[,type]) replace current frames with new file
v.append(file[,type]) append file to current frame(s)
v.replace(file[,type]) replace current frames with new file
v.append(file[,type]) append file to current frame(s)
v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
v.frame(frame) set current frame
v.flush() flush pending input to VMD and update GUI
v.read(file) read Tcl script file (e.g. saved state)
v.enter() enter interactive shell
v.debug([True|False]) display generated VMD script commands?
v.frame(frame) set current frame
v.flush() flush pending input to VMD and update GUI
v.read(file) read Tcl script file (e.g. saved state)
v.enter() enter interactive shell
v.debug([True|False]) display generated VMD script commands?
"""
# History
@ -71,7 +71,7 @@ except ImportError:
# Class definition
class vmd:
# --------------------------------------------------------------------
def __init__(self):
@ -103,7 +103,7 @@ class vmd:
# open pipe to vmd and wait until we have a prompt
self.VMD = pexpect.spawn(self.vmdexe)
self.VMD.expect('vmd >')
# --------------------------------------------------------------------
# post command to vmd and wait until the prompt returns.
def __call__(self,command):
@ -113,7 +113,7 @@ class vmd:
if self.debugme:
print("call+result:"+self.VMD.before)
return
# --------------------------------------------------------------------
# exit VMD
def stop(self):
@ -198,7 +198,7 @@ class vmd:
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
self.flush()
# --------------------------------------------------------------------
# replace all frames of a molecule with those from a given file
def update(self,filename,filetype='lammpstrj'):
@ -209,7 +209,7 @@ class vmd:
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
self.flush()
# --------------------------------------------------------------------
# add or overwrite coordinates with coordinates in a snapshot
def set(self,snap,x,y,z,append=True):

2
python/examples/pylammps/elastic/README
View File

@ -1,4 +1,4 @@
conversion of lammps scripts to python code using PyLammps interface
Example for elastic.py
Example for elastic.py
python elastic.py Au.data EAM_Dynamo_Ackland_1987_Au__MO_754413982908_000 Au

6
python/examples/split.py
View File

@ -32,7 +32,7 @@ nprocs = comm.Get_size()
if me < nprocs // 2: color = 0
else: color = 1
split = comm.Split(color,key=0)
if color == 0:
@ -69,12 +69,12 @@ else:
# could run a 2nd calculation on second partition
# with different LAMMPS instance or another code
# in this case, just sleep on second partition
import time
time.sleep(2)
print("Calculation on partition 1 complete")
# shutdown mpi4py
comm.Barrier()
MPI.Finalize()

2
python/examples/viz_gl.py
View File

@ -50,7 +50,7 @@ ntimestep = 0
if me == 0:
tkroot = None
try:
try:
import Tkinter
except:
import tkinter as Tkinter

4
python/examples/viz_pymol.py
View File

@ -63,7 +63,7 @@ if me == 0:
p.single(ntimestep)
pm.load("tmp.pdb")
pm.show("spheres","tmp")
# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
while ntimestep < nsteps:
@ -75,7 +75,7 @@ while ntimestep < nsteps:
p.single(ntimestep)
pm.load("tmp.pdb")
pm.forward()
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via mpi4py

5
python/lammps/constants.py
View File

@ -22,7 +22,8 @@ LAMMPS_INT64 = 4
LAMMPS_INT64_2D = 5
LAMMPS_STRING = 6
# these must be kept in sync with the enums in library.h
# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i
# and the constants in fortran/lammps.f90
LMP_STYLE_GLOBAL = 0
LMP_STYLE_ATOM = 1
LMP_STYLE_LOCAL = 2
@ -42,6 +43,8 @@ LMP_ERROR_UNIVERSE = 8
LMP_VAR_EQUAL = 0
LMP_VAR_ATOM = 1
LMP_VAR_VECTOR = 2
LMP_VAR_STRING = 3
# -------------------------------------------------------------------------

47
python/lammps/core.py
View File

@ -301,6 +301,8 @@ class lammps(object):
self.lib.lammps_extract_fix.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int, c_int]
self.lib.lammps_extract_variable.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_extract_variable_datatype.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_variable_datatype.restype = c_int
self.lib.lammps_fix_external_get_force.argtypes = [c_void_p, c_char_p]
self.lib.lammps_fix_external_get_force.restype = POINTER(POINTER(c_double))
@ -1083,21 +1085,23 @@ class lammps(object):
# for vector, must copy nlocal returned values to local c_double vector
# memory was allocated by library interface function
def extract_variable(self, name, group=None, vartype=LMP_VAR_EQUAL):
def extract_variable(self, name, group=None, vartype=None):
""" Evaluate a LAMMPS variable and return its data
This function is a wrapper around the function
:cpp:func:`lammps_extract_variable` of the C-library interface,
:cpp:func:`lammps_extract_variable` of the C library interface,
evaluates variable name and returns a copy of the computed data.
The memory temporarily allocated by the C-interface is deleted
after the data is copied to a Python variable or list.
The variable must be either an equal-style (or equivalent)
variable or an atom-style variable. The variable type has to
provided as ``vartype`` parameter which may be one of two constants:
``LMP_VAR_EQUAL`` or ``LMP_VAR_ATOM``; it defaults to
equal-style variables.
The group parameter is only used for atom-style variables and
defaults to the group "all" if set to ``None``, which is the default.
variable or an atom-style variable. The variable type can be
provided as the ``vartype`` parameter, which may be one of several
constants: ``LMP_VAR_EQUAL``, ``LMP_VAR_ATOM``, ``LMP_VAR_VECTOR``,
or ``LMP_VAR_STRING``. If omitted or ``None``, LAMMPS will determine its
value for you based on a call to
:cpp:func:`lammps_extract_variable_datatype` from the C library interface.
The group parameter is only used for atom-style variables and defaults to
the group "all".
:param name: name of the variable to execute
:type name: string
@ -1111,6 +1115,8 @@ class lammps(object):
if name: name = name.encode()
else: return None
if group: group = group.encode()
if vartype is None :
vartype = self.lib.lammps_extract_variable_datatype(self.lmp, name)
if vartype == LMP_VAR_EQUAL:
self.lib.lammps_extract_variable.restype = POINTER(c_double)
with ExceptionCheck(self):
@ -1130,6 +1136,31 @@ class lammps(object):
self.lib.lammps_free(ptr)
else: return None
return result
elif vartype == LMP_VAR_VECTOR :
nvector = 0
self.lib.lammps_extract_variable.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_variable(self.lmp,name,
'LMP_SIZE_VECTOR'.encode())
if ptr :
nvector = ptr[0]
self.lib.lammps_free(ptr)
else :
return None
self.lib.lammps_extract_variable.restype = POINTER(c_double)
result = (c_double*nvector)()
values = self.lib.lammps_extract_variable(self.lmp,name,group)
if values :
for i in range(nvector) :
result[i] = values[i]
# do NOT free the values pointer (points to internal vector data)
return result
else :
return None
elif vartype == LMP_VAR_STRING :
self.lib.lammps_extract_variable.restype = c_char_p
with ExceptionCheck(self) :
ptr = self.lib.lammps_extract_variable(self.lmp, name, group)
return ptr.decode('utf-8')
return None
# -------------------------------------------------------------------------

415
src/library.cpp
View File

@ -949,7 +949,8 @@ int lammps_get_mpi_comm(void *handle)
This function will retrieve or compute global properties. In contrast to
:cpp:func:`lammps_get_thermo` this function returns an ``int``. The
following tables list the currently supported keyword. If a keyword is
not recognized, the function returns -1.
not recognized, the function returns -1. The integer sizes functions may
be called without a valid LAMMPS object handle (it is ignored).
* :ref:`Integer sizes <extract_integer_sizes>`
* :ref:`System status <extract_system_status>`
@ -1145,7 +1146,7 @@ int lammps_extract_setting(void *handle, const char *keyword)
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.
to then decide how to cast the ``void *`` pointer and access the data.
.. versionadded:: 18Sep2020
@ -1622,7 +1623,7 @@ void *lammps_extract_global(void *handle, const char *name)
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.
to then decide how to cast the ``void *`` pointer and access the data.
.. versionadded:: 18Sep2020
@ -2043,16 +2044,19 @@ void *lammps_extract_fix(void *handle, const char *id, int style, int type,
This function returns a pointer to data from a LAMMPS :doc:`variable`
identified by its name. When the variable is either an *equal*\ -style
compatible or an *atom*\ -style variable the variable is evaluated and
the corresponding value(s) returned. Variables of style *internal*
are compatible with *equal*\ -style variables and so are *python*\
-style variables, if they return a numeric value. For other
variable styles their string value is returned. The function returns
compatible variable, a *vector*\ -style variable, or an *atom*\ -style
variable, the variable is evaluated and the corresponding value(s) returned.
Variables of style *internal* are compatible with *equal*\ -style variables and
so are *python*\ -style variables, if they return a numeric value. For other
variable styles, their string value is returned. The function returns
``NULL`` when a variable of the provided *name* is not found or of an
incompatible style. The *group* argument is only used for *atom*\
-style variables and ignored otherwise. If set to ``NULL`` when
extracting data from and *atom*\ -style variable, the group is assumed
to be "all".
-style variables and ignored otherwise, with one exception: for style *vector*,
if *group* is "GET_VECTOR_SIZE", the returned pointer will yield the length
of the vector to be returned when dereferenced. This pointer must be
deallocated after the value is read to avoid a memory leak.
If *group* is set to ``NULL`` when extracting data from an *atom*\ -style
variable, the group is assumed to be "all".
When requesting data from an *equal*\ -style or compatible variable
this function allocates storage for a single double value, copies the
@ -2066,15 +2070,23 @@ use to avoid a memory leak. Example:
double value = *dptr;
lammps_free((void *)dptr);
For *atom*\ -style variables the data returned is a pointer to an
For *atom*\ -style variables, the return value is a pointer to an
allocated block of storage of double of the length ``atom->nlocal``.
Since the data is returned a copy, the location will persist, but its
content will not be updated, in case the variable is re-evaluated.
To avoid a memory leak this pointer needs to be freed after use in
Since the data returned are a copy, the location will persist, but its
content will not be updated in case the variable is re-evaluated.
To avoid a memory leak, this pointer needs to be freed after use in
the calling program.
For *vector*\ -style variables, the returned pointer is to actual LAMMPS data.
The pointer should not be deallocated. Its length depends on the variable,
compute, or fix data used to construct the *vector*\ -style variable.
This length can be fetched by calling this function with *group* set to the
constant "LMP_SIZE_VECTOR", which returns a ``void *`` pointer that can be
dereferenced to an integer that is the length of the vector. This pointer
needs to be deallocated when finished with it to avoid memory leaks.
For other variable styles the returned pointer needs to be cast to
a char pointer.
a char pointer. It should not be deallocated.
.. code-block:: c
@ -2084,10 +2096,10 @@ a char pointer.
.. note::
LAMMPS cannot easily check if it is valid to access the data
referenced by the variables, e.g. computes or fixes or thermodynamic
info, so it may fail with an error. The caller has to make certain,
that the data is extracted only when it safe to evaluate the variable
and thus an error and crash is avoided.
referenced by the variables (e.g., computes, fixes, or thermodynamic
info), so it may fail with an error. The caller has to make certain
that the data are extracted only when it safe to evaluate the variable
and thus an error or crash are avoided.
\endverbatim
*
@ -2118,6 +2130,15 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
auto vector = (double *) malloc(nlocal*sizeof(double));
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector;
} else if (lmp->input->variable->vectorstyle(ivar)) {
double *values = nullptr;
int nvector = lmp->input->variable->compute_vector(ivar, &values);
if ( group != nullptr && strcmp(group,"LMP_SIZE_VECTOR") == 0 ) {
int* nvecptr = (int *) malloc(sizeof(int));
*nvecptr = nvector;
return (void *) nvecptr;
} else
return (void *) values;
} else {
return lmp->input->variable->retrieve(name);
}
@ -2130,6 +2151,49 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
/* ---------------------------------------------------------------------- */
/** Get data type of a LAMMPS variable.
*
\verbatim embed:rst
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:: TBD
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param name string with the name of the extracted variable
* \return integer constant encoding the data type of the property
* or -1 if not found.
**/
int lammps_extract_variable_datatype(void *handle, const char *name)
{
auto lmp = (LAMMPS*) handle;
BEGIN_CAPTURE
{
int ivar = lmp->input->variable->find(name);
if ( ivar < 0 ) return -1;
if (lmp->input->variable->equalstyle(ivar))
return LMP_VAR_EQUAL;
else if (lmp->input->variable->atomstyle(ivar))
return LMP_VAR_ATOM;
else if (lmp->input->variable->vectorstyle(ivar))
return LMP_VAR_VECTOR;
else
return LMP_VAR_STRING;
}
END_CAPTURE
return -1;
}
/* ---------------------------------------------------------------------- */
/** Set the value of a string-style variable.
*
* This function assigns a new value from the string str to the
@ -2159,21 +2223,38 @@ int lammps_set_variable(void *handle, char *name, char *str)
// Library functions for scatter/gather operations of data
// ----------------------------------------------------------------------
/** Gather the named atom-based entity for all atoms across all processors,
* in order.
*
\verbatim embed:rst
This subroutine gathers data for all atoms and stores them in a
one-dimensional array allocated by the user. The data will be ordered by
atom ID, which requires consecutive atom IDs (1 to *natoms*\ ). If you need
a similar array but have non-consecutive atom IDs, see
:cpp:func:`lammps_gather_atoms_concat`; for a similar array but for a subset
of atoms, see :cpp:func:`lammps_gather_atoms_subset`.
The *data* array will be ordered in groups of *count* values, sorted by atom ID
(e.g., if *name* is *x* and *count* = 3, then *data* = x[0][0], x[0][1],
x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`);
*data* must be pre-allocated by the caller to length (*count* :math:`\times`
*natoms*), as queried by :cpp:func:`lammps_get_natoms`,
:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`.
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param name desired quantity (e.g., *x* or *charge*)
* \param type 0 for ``int`` values, 1 for ``double`` values
* \param count number of per-atom values (e.g., 1 for *type* or *charge*,
* 3 for *x* or *f*); use *count* = 3 with *image* if you want
* a single image flag unpacked into (*x*,*y*,*z*) components.
* \param data per-atom values packed in a 1-dimensional array of length
* *natoms* \* *count*.
*
*/
/* ----------------------------------------------------------------------
gather the named atom-based entity for all atoms
return it in user-allocated data
data will be ordered by atom ID
requirement for consecutive atom IDs (1 to N)
see gather_atoms_concat() to return data for all atoms, unordered
see gather_atoms_subset() to return data for only a subset of atoms
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
alloc and zero count*Natom length vector
loop over Nlocal to fill vector with my values
@ -2294,23 +2375,43 @@ void lammps_gather_atoms(void *handle, char *name, int type, int count, void *da
END_CAPTURE
}
/** Gather the named atom-based entity for all atoms across all processors,
* unordered.
*
\verbatim embed:rst
This subroutine gathers data for all atoms and stores them in a
one-dimensional array allocated by the user. The data will be a concatenation
of chunks from each processor's owned atoms, in whatever order the atoms are
in on each processor. This process has no requirement that the atom IDs be
consecutive. If you need the ID of each atom, you can do another
:cpp:func:`lammps_gather_atoms_concat` call with *name* set to ``id``.
If you have consecutive IDs and want the data to be in order, use
:cpp:func:`lammps_gather_atoms`; for a similar array but for a subset
of atoms, use :cpp:func:`lammps_gather_atoms_subset`.
The *data* array will be in groups of *count* values, with *natoms*
groups total, but not in order by atom ID (e.g., if *name* is *x* and *count*
is 3, then *data* might be something like = x[10][0], x[10][1], x[10][2],
x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`); *data* must be
pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as
queried by :cpp:func:`lammps_get_natoms`,
:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`.
\endverbatim
*
* \param handle: pointer to a previously created LAMMPS instance
* \param name: desired quantity (e.g., *x* or *charge*\ )
* \param type: 0 for ``int`` values, 1 for ``double`` values
* \param count: number of per-atom values (e.g., 1 for *type* or *charge*,
* 3 for *x* or *f*); use *count* = 3 with "image" if you want
* single image flags unpacked into (*x*,*y*,*z*)
* \param data: per-atom values packed in a 1-dimensional array of length
* *natoms* \* *count*.
*
*/
/* ----------------------------------------------------------------------
gather the named atom-based entity for all atoms
return it in user-allocated data
data will be a concatenation of chunks of each proc's atoms,
in whatever order the atoms are on each proc
no requirement for consecutive atom IDs (1 to N)
can do a gather_atoms_concat for "id" if need to know atom IDs
see gather_atoms() to return data ordered by consecutive atom IDs
see gather_atoms_subset() to return data for only a subset of atoms
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
Allgather Nlocal atoms from each proc into data
------------------------------------------------------------------------- */
@ -2440,23 +2541,40 @@ void lammps_gather_atoms_concat(void *handle, char *name, int type, int count, v
END_CAPTURE
}
/** Gather the named atom-based entity for a subset of atoms.
*
\verbatim embed:rst
This subroutine gathers data for the requested atom IDs and stores them in a
one-dimensional array allocated by the user. The data will be ordered by atom
ID, but there is no requirement that the IDs be consecutive. If you wish to
return a similar array for *all* the atoms, use :cpp:func:`lammps_gather_atoms`
or :cpp:func:`lammps_gather_atoms_concat`.
The *data* array will be in groups of *count* values, sorted by atom ID
in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and
*ids* is {100, 57, 210}, then *data* might look like {x[100][0], x[100][1],
x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], :math:`\dots`);
*ids* must be provided by the user with length *ndata*, and
*data* must be pre-allocated by the caller to length
(*count* :math:`\times` *ndata*).
\endverbatim
*
* \param handle: pointer to a previously created LAMMPS instance
* \param name: desired quantity (e.g., *x* or *charge*)
* \param type: 0 for ``int`` values, 1 for ``double`` values
* \param count: number of per-atom values (e.g., 1 for *type* or *charge*,
* 3 for *x* or *f*); use *count* = 3 with "image" if you want
* single image flags unpacked into (*x*,*y*,*z*)
* \param ndata: number of atoms for which to return data (can be all of them)
* \param ids: list of *ndata* atom IDs for which to return data
* \param data: per-atom values packed in a 1-dimensional array of length
* *ndata* \* *count*.
*
*/
/* ----------------------------------------------------------------------
gather the named atom-based entity for a subset of atoms
return it in user-allocated data
data will be ordered by requested atom IDs
no requirement for consecutive atom IDs (1 to N)
see gather_atoms() to return data for all atoms, ordered by consecutive IDs
see gather_atoms_concat() to return data for all atoms, unordered
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz
ndata = # of atoms to return data for (could be all atoms)
ids = list of Ndata atom IDs to return data for
return atom-based values in 1d data, ordered by count, then by atom
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be pre-allocated by caller to correct length
correct length = count*Ndata
method:
alloc and zero count*Ndata length vector
loop over Ndata to fill vector with my values
@ -2477,15 +2595,16 @@ void lammps_gather_atoms_subset(void *handle, char *name, int type, int count,
int i,j,m,offset;
tagint id;
// error if tags are not defined
// error if tags are not defined or no atom map
// NOTE: test that name = image or ids is not a 64-bit int in code?
int flag = 0;
if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms_subset");
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms_subset: atoms must have mappable ids");
return;
}
@ -2586,18 +2705,35 @@ void lammps_gather_atoms_subset(void *handle, char *name, int type, int count,
END_CAPTURE
}
/** Scatter the named atom-based entities in *data* to all processors.
*
\verbatim embed:rst
This subroutine takes data stored in a one-dimensional array supplied by the
user and scatters them to all atoms on all processors. The data must be
ordered by atom ID, with the requirement that the IDs be consecutive.
Use :cpp:func:`lammps_scatter_atoms_subset` to scatter data for some (or all)
atoms, unordered.
The *data* array needs to be ordered in groups of *count* values, sorted by
atom ID (e.g., if *name* is *x* and *count* = 3, then
*data* = x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0],
:math:`\dots`); *data* must be of length (*count* :math:`\times` *natoms*).
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param name desired quantity (e.g., *x* or *charge*)
* \param type 0 for ``int`` values, 1 for ``double`` values
* \param count number of per-atom values (e.g., 1 for *type* or *charge*,
* 3 for *x* or *f*); use *count* = 3 with *image* if you have
* a single image flag packed into (*x*,*y*,*z*) components.
* \param data per-atom values packed in a 1-dimensional array of length
* *natoms* \* *count*.
*
*/
/* ----------------------------------------------------------------------
scatter the named atom-based entity in data to all atoms
data is ordered by atom ID
requirement for consecutive atom IDs (1 to N)
see scatter_atoms_subset() to scatter data for some (or all) atoms, unordered
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" for xyz to be packed into single image flag
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be correct length = count*Natoms, as queried by get_natoms()
method:
loop over Natoms, if I own atom ID, set its values from data
------------------------------------------------------------------------- */
@ -2624,7 +2760,7 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms: ids must exist, be consecutive, and be mapped");
return;
}
@ -2702,19 +2838,51 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d
END_CAPTURE
}
/** Scatter the named atom-based entities in *data* from a subset of atoms
* to all processors.
*
\verbatim embed:rst
This subroutine takes data stored in a one-dimensional array supplied by the
user and scatters them to a subset of atoms on all processors. The array
*data* contains data associated with atom IDs, but there is no requirement that
the IDs be consecutive, as they are provided in a separate array.
Use :cpp:func:`lammps_scatter_atoms` to scatter data for all atoms, in order.
The *data* array needs to be organized in groups of *count* values, with the
groups in the same order as the array *ids*. For example, if you want *data*
to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2],
x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would
be {1, 100, 57}.
\endverbatim
*
* \param handle: pointer to a previously created LAMMPS instance
* \param name: desired quantity (e.g., *x* or *charge*)
* \param type: 0 for ``int`` values, 1 for ``double`` values
* \param count: number of per-atom values (e.g., 1 for *type* or *charge*,
* 3 for *x* or *f*); use *count* = 3 with "image" if you have
* all the image flags packed into (*xyz*)
* \param ndata: number of atoms listed in *ids* and *data* arrays
* \param ids: list of *ndata* atom IDs to scatter data to
* \param data per-atom values packed in a 1-dimensional array of length
* *ndata* \* *count*.
*
*/
/* ----------------------------------------------------------------------
scatter the named atom-based entity in data to a subset of atoms
data is ordered by provided atom IDs
no requirement for consecutive atom IDs (1 to N)
see scatter_atoms() to scatter data for all atoms, ordered by consecutive IDs
name = desired quantity, e.g. x or charge
name = desired quantity (e.g., x or charge)
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" for xyz to be packed into single image flag
ndata = # of atoms in ids and data (could be all atoms)
ids = list of Ndata atom IDs to scatter data to
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be correct length = count*Ndata
method:
loop over Ndata, if I own atom ID, set its values from data
@ -2743,7 +2911,7 @@ void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count,
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset");
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset: atoms must have mapped ids");
return;
}
@ -2904,7 +3072,7 @@ Below is a brief C code demonstrating accessing this collected bond information.
void lammps_gather_bonds(void *handle, void *data)
{
auto lmp = (LAMMPS *)handle;
auto lmp = (LAMMPS *) handle;
BEGIN_CAPTURE {
void *val = lammps_extract_global(handle,"nbonds");
bigint nbonds = *(bigint *)val;
@ -2951,10 +3119,10 @@ void lammps_gather_bonds(void *handle, void *data)
"d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
@ -3186,10 +3354,10 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
"d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
@ -3438,10 +3606,10 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
"d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
@ -3465,11 +3633,12 @@ void lammps_gather_subset(void *handle, char *name,
int i,j,m,offset,ltype;
tagint id;
// error if tags are not defined or not consecutive
// error if tags are not defined or no atom map
int flag = 0;
if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == Atom::MAP_NONE) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_subset");
@ -3686,10 +3855,10 @@ void lammps_gather_subset(void *handle, char *name,
"d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" if want single image flag unpacked into xyz
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be pre-allocated by caller to correct length
correct length = count*Natoms, as queried by get_natoms()
method:
@ -3904,12 +4073,12 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
"f_fix", "c_compute" for fixes / computes
will return error if fix/compute doesn't isn't atom-based
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
count = # of per-atom values (e.g., 1 for type or charge, 3 for x or f)
use count = 3 with "image" for xyz to be packed into single image flag
ndata = # of atoms in ids and data (could be all atoms)
ids = list of Ndata atom IDs to scatter data to
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
(e.g., x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...)
data must be correct length = count*Ndata
method:
loop over Ndata, if I own atom ID, set its values from data
@ -4152,8 +4321,8 @@ boundaries atoms will be wrapped back into the simulation cell and its
image flags adjusted accordingly, unless explicit image flags are
provided.
The function returns the number of atoms created or -1 on failure, e.g.
when called before as box has been created.
The function returns the number of atoms created or -1 on failure (e.g.,
when called before as box has been created).
Coordinates and velocities have to be given in a 1d-array in the order
X(1),Y(1),Z(1),X(2),Y(2),Z(2),...,X(N),Y(N),Z(N).
@ -4358,7 +4527,7 @@ int lammps_find_fix_neighlist(void *handle, const char *id, int reqid) {
* multiple requests from the same compute
* \return return neighbor list index if found, otherwise -1 */
int lammps_find_compute_neighlist(void* handle, const char *id, int reqid) {
int lammps_find_compute_neighlist(void *handle, const char *id, int reqid) {
auto lmp = (LAMMPS *) handle;
auto compute = lmp->modify->get_compute_by_id(id);
if (!compute) return -1;
@ -4511,7 +4680,7 @@ int lammps_config_has_mpi_support()
* files via a pipe to gzip or similar compression programs
\verbatim embed:rst
Several LAMMPS commands (e.g. :doc:`read_data`, :doc:`write_data`,
Several LAMMPS commands (e.g., :doc:`read_data`, :doc:`write_data`,
:doc:`dump styles atom, custom, and xyz <dump>`) support reading and
writing compressed files via creating a pipe to the ``gzip`` program.
This function checks whether this feature was :ref:`enabled at compile
@ -4531,8 +4700,8 @@ int lammps_config_has_gzip_support() {
\verbatim embed:rst
The LAMMPS :doc:`dump style image <dump_image>` supports writing multiple
image file formats. Most of them need, however, support from an external
library and using that has to be :ref:`enabled at compile time <graphics>`.
image file formats. Most of them, however, need support from an external
library, and using that has to be :ref:`enabled at compile time <graphics>`.
This function checks whether support for the `PNG image file format
<https://en.wikipedia.org/wiki/Portable_Network_Graphics>`_ is available
in the current LAMMPS library.
@ -4550,8 +4719,8 @@ int lammps_config_has_png_support() {
\verbatim embed:rst
The LAMMPS :doc:`dump style image <dump_image>` supports writing multiple
image file formats. Most of them need, however, support from an external
library and using that has to be :ref:`enabled at compile time <graphics>`.
image file formats. Most of them, however, need support from an external
library, and using that has to be :ref:`enabled at compile time <graphics>`.
This function checks whether support for the `JPEG image file format
<https://jpeg.org/jpeg/>`_ is available in the current LAMMPS library.
\endverbatim
@ -4568,7 +4737,7 @@ int lammps_config_has_jpeg_support() {
\verbatim embed:rst
The LAMMPS :doc:`dump style movie <dump_image>` supports generating movies
from images on-the-fly via creating a pipe to the
from images on-the-fly via creating a pipe to the
`ffmpeg <https://ffmpeg.org/ffmpeg/>`_ program.
This function checks whether this feature was :ref:`enabled at compile time <graphics>`.
It does **not** check whether the ``ffmpeg`` itself is installed and usable.
@ -4582,14 +4751,14 @@ int lammps_config_has_ffmpeg_support() {
/* ---------------------------------------------------------------------- */
/** Check whether LAMMPS errors will throw a C++ exception
/** Check whether LAMMPS errors will throw C++ exceptions.
*
\verbatim embed:rst
In case of errors LAMMPS will either abort or throw a C++ exception.
In case of an error, LAMMPS will either abort or throw a C++ exception.
The latter has to be :ref:`enabled at compile time <exceptions>`.
This function checks if exceptions were enabled.
When using the library interface and C++ exceptions are enabled,
When using the library interface with C++ exceptions enabled,
the library interface functions will "catch" them and the
error status can then be checked by calling
:cpp:func:`lammps_has_error` and the most recent error message
@ -4608,10 +4777,10 @@ int lammps_config_has_exceptions() {
/* ---------------------------------------------------------------------- */
/** Check if a specific package has been included in LAMMPS
/** Check whether a specific package has been included in LAMMPS
*
\verbatim embed:rst
This function checks if the LAMMPS library in use includes the
This function checks whether the LAMMPS library in use includes the
specific :doc:`LAMMPS package <Packages>` provided as argument.
\endverbatim
*
@ -5183,8 +5352,8 @@ 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 e.g. :cpp:func:`lammps_get_natoms` to obtain the number
of local atoms `nlocal` and then assume the dimensions of the returned
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
@ -5470,7 +5639,7 @@ void lammps_fix_external_set_vector_length(void *handle, const char *id, int len
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
within LAMMPS input commands (e.g. fix ave/time or variables) when used
within LAMMPS input commands (e.g., fix ave/time or variables) when used
in a vector context.
This function needs to be called **after** a call to
@ -5568,7 +5737,7 @@ int lammps_is_running(void *handle)
return lmp->update->whichflag;
}
/** Force a timeout to cleanly stop an ongoing run
/** Force a timeout to stop an ongoing run cleanly.
*
* This function can be used from signal handlers or multi-threaded
* applications to cleanly terminate an ongoing run.
@ -5594,9 +5763,9 @@ has thrown a :ref:`C++ exception <exceptions>`.
.. note::
This function will always report "no error" when the LAMMPS library
has been compiled without ``-DLAMMPS_EXCEPTIONS`` which turns fatal
errors aborting LAMMPS into a C++ exceptions. You can use the library
function :cpp:func:`lammps_config_has_exceptions` to check if this is
has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
errors aborting LAMMPS into C++ exceptions. You can use the library
function :cpp:func:`lammps_config_has_exceptions` to check whether this is
the case.
\endverbatim
*
@ -5605,8 +5774,8 @@ has thrown a :ref:`C++ exception <exceptions>`.
*/
int lammps_has_error(void *handle) {
#ifdef LAMMPS_EXCEPTIONS
LAMMPS * lmp = (LAMMPS *) handle;
Error * error = lmp->error;
LAMMPS *lmp = (LAMMPS *) handle;
Error *error = lmp->error;
return (error->get_last_error().empty()) ? 0 : 1;
#else
return 0;
@ -5626,15 +5795,15 @@ error message is longer, it will be truncated accordingly. The return
value of the function corresponds to the kind of error: a "1" indicates
an error that occurred on all MPI ranks and is often recoverable, while
a "2" indicates an abort that would happen only in a single MPI rank
and thus may not be recoverable as other MPI ranks may be waiting on
and thus may not be recoverable, as other MPI ranks may be waiting on
the failing MPI ranks to send messages.
.. note::
This function will do nothing when the LAMMPS library has been
compiled without ``-DLAMMPS_EXCEPTIONS`` which turns errors aborting
LAMMPS into a C++ exceptions. You can use the library function
:cpp:func:`lammps_config_has_exceptions` to check if this is the case.
compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
LAMMPS into C++ exceptions. You can use the library function
:cpp:func:`lammps_config_has_exceptions` to check whether this is the case.
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.

25
src/library.h
View File

@ -40,7 +40,8 @@
/** Data type constants for extracting data from atoms, computes and fixes
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_DATATYPE_CONST {
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
@ -54,7 +55,8 @@ enum _LMP_DATATYPE_CONST {
/** Style constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_STYLE_CONST {
LMP_STYLE_GLOBAL = 0, /*!< return global data */
@ -64,7 +66,8 @@ enum _LMP_STYLE_CONST {
/** Type and size constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_TYPE_CONST {
LMP_TYPE_SCALAR = 0, /*!< return scalar */
@ -77,7 +80,8 @@ enum _LMP_TYPE_CONST {
/** Error codes to select the suitable function in the Error class
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_ERROR_CONST {
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
@ -87,6 +91,18 @@ enum _LMP_ERROR_CONST {
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
};
/** Variable style constants for extracting data from variables.
*
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_VAR_CONST {
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
};
/* Ifdefs to allow this file to be included in C and C++ programs */
#ifdef __cplusplus
@ -153,6 +169,7 @@ void *lammps_extract_atom(void *handle, const char *name);
void *lammps_extract_compute(void *handle, const char *, int, int);
void *lammps_extract_fix(void *handle, const char *, int, int, int, int);
void *lammps_extract_variable(void *handle, const char *, const char *);
int lammps_extract_variable_datatype(void *handle, const char *name);
int lammps_set_variable(void *, char *, char *);
/* ----------------------------------------------------------------------

4
tools/coding_standard/whitespace.py
View File

@ -24,11 +24,13 @@ include:
- cmake/**
- doc
- doc/src/**
- python
- fortran/**
- python/**
- src/**
- lib/**
- tools/coding_standard
- tools/python
- unittest/**
exclude:
- lib/colvars/Install.py
- lib/gpu/geryon/file_to_cstr.sh

183
tools/swig/lammps.i
View File

@ -22,37 +22,69 @@
%{
/** Data type constants for extracting data from atoms, computes and fixes
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_DATATYPE_CONST {
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
};
/** Style constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_STYLE_CONST {
LMP_STYLE_GLOBAL=0, /*!< return global data */
LMP_STYLE_ATOM =1, /*!< return per-atom data */
LMP_STYLE_LOCAL =2 /*!< return local data */
LMP_STYLE_GLOBAL = 0, /*!< return global data */
LMP_STYLE_ATOM = 1, /*!< return per-atom data */
LMP_STYLE_LOCAL = 2 /*!< return local data */
};
/** Type and size constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_TYPE_CONST {
LMP_TYPE_SCALAR=0, /*!< return scalar */
LMP_TYPE_VECTOR=1, /*!< return vector */
LMP_TYPE_ARRAY =2, /*!< return array */
LMP_SIZE_VECTOR=3, /*!< return length of vector */
LMP_SIZE_ROWS =4, /*!< return number of rows */
LMP_SIZE_COLS =5 /*!< return number of columns */
LMP_TYPE_SCALAR = 0, /*!< return scalar */
LMP_TYPE_VECTOR = 1, /*!< return vector */
LMP_TYPE_ARRAY = 2, /*!< return array */
LMP_SIZE_VECTOR = 3, /*!< return length of vector */
LMP_SIZE_ROWS = 4, /*!< return number of rows */
LMP_SIZE_COLS = 5 /*!< return number of columns */
};
/** Error codes to select the suitable function in the Error class
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_ERROR_CONST {
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
LMP_ERROR_ONE = 1, /*!< called from one MPI rank */
LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */
LMP_ERROR_WORLD = 4, /*!< error on Comm::world */
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
};
/** Variable style constants for extracting data from variables.
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_VAR_CONST {
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
};
/*
@ -65,10 +97,13 @@ extern void lammps_mpi_init();
extern void lammps_mpi_finalize();
extern void lammps_kokkos_finalize();
extern void lammps_python_finalize();
extern void lammps_error(void *handle, int error_type, const char *error_text);
extern void lammps_file(void *handle, const char *file);
extern char *lammps_command(void *handle, const char *cmd);
extern void lammps_commands_list(void *handle, int ncmd, const char **cmds);
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_extract_box(void *handle, double *boxlo, double *boxhi,
@ -81,12 +116,16 @@ extern int lammps_get_mpi_comm(void *handle);
extern int lammps_extract_setting(void *handle, const char *keyword);
extern int lammps_extract_global_datatype(void *handle, const char *name);
extern void *lammps_extract_global(void *handle, const char *name);
extern int lammps_extract_atom_datatype(void *handle, const char *name);
extern void *lammps_extract_atom(void *handle, const char *name);
extern void *lammps_extract_compute(void *handle, char *id, int, int);
extern void *lammps_extract_fix(void *handle, char *, int, int, int, int);
extern void *lammps_extract_variable(void *handle, char *, char *);
extern int lammps_extract_variable_datatype(void *handle, const char *name);
extern int lammps_set_variable(void *, char *, char *);
extern void lammps_gather_atoms(void *, char *, int, int, void *);
extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
@ -107,6 +146,7 @@ extern int lammps_find_fix_neighlist(void*, char *, int);
extern int lammps_find_compute_neighlist(void*, char *, int);
extern int lammps_neighlist_num_elements(void*, int);
extern void lammps_neighlist_element_neighbors(void *, int, int, int *, int *, int ** );
extern int lammps_version(void *handle);
extern void lammps_get_os_info(char *buffer, int buf_size);
extern int lammps_config_has_mpi_support();
@ -151,46 +191,79 @@ extern void lammps_fix_external_set_virial_global(void *handle, const char *id
extern void lammps_fix_external_set_vector_length(void *handle, const char *id, int len);
extern void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val);
extern void lammps_flush_buffers(void *ptr);
extern void lammps_free(void *ptr);
extern int lammps_is_running(void *handle);
extern void lammps_force_timeout(void *handle);
extern int lammps_has_error(void *handle);
extern int lammps_get_last_error_message(void *handle, char *buffer, int buf_size);
extern int lammps_python_api_version();
extern void lammps_flush_buffers(void *ptr);
%}
/** Data type constants for extracting data from atoms, computes and fixes
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_DATATYPE_CONST {
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
};
/** Style constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_STYLE_CONST {
LMP_STYLE_GLOBAL=0, /*!< return global data */
LMP_STYLE_ATOM =1, /*!< return per-atom data */
LMP_STYLE_LOCAL =2 /*!< return local data */
LMP_STYLE_GLOBAL = 0, /*!< return global data */
LMP_STYLE_ATOM = 1, /*!< return per-atom data */
LMP_STYLE_LOCAL = 2 /*!< return local data */
};
/** Type and size constants for extracting data from computes and fixes.
*
* Must be kept in sync with the equivalent constants in lammps/constants.py */
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_TYPE_CONST {
LMP_TYPE_SCALAR=0, /*!< return scalar */
LMP_TYPE_VECTOR=1, /*!< return vector */
LMP_TYPE_ARRAY =2, /*!< return array */
LMP_SIZE_VECTOR=3, /*!< return length of vector */
LMP_SIZE_ROWS =4, /*!< return number of rows */
LMP_SIZE_COLS =5 /*!< return number of columns */
LMP_TYPE_SCALAR = 0, /*!< return scalar */
LMP_TYPE_VECTOR = 1, /*!< return vector */
LMP_TYPE_ARRAY = 2, /*!< return array */
LMP_SIZE_VECTOR = 3, /*!< return length of vector */
LMP_SIZE_ROWS = 4, /*!< return number of rows */
LMP_SIZE_COLS = 5 /*!< return number of columns */
};
/** Error codes to select the suitable function in the Error class
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_ERROR_CONST {
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
LMP_ERROR_ONE = 1, /*!< called from one MPI rank */
LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */
LMP_ERROR_WORLD = 4, /*!< error on Comm::world */
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
};
/** Variable style constants for extracting data from variables.
*
* Must be kept in sync with the equivalent constants in src/library.h,
* python/lammps/constants.py, and fortran/lammps.f90 */
enum _LMP_VAR_CONST {
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
};
/*
@ -203,10 +276,13 @@ extern void lammps_mpi_init();
extern void lammps_mpi_finalize();
extern void lammps_kokkos_finalize();
extern void lammps_python_finalize();
extern void lammps_error(void *handle, int error_type, const char *error_text);
extern void lammps_file(void *handle, const char *file);
extern char *lammps_command(void *handle, const char *cmd);
extern void lammps_commands_list(void *handle, int ncmd, const char **cmds);
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_extract_box(void *handle, double *boxlo, double *boxhi,
@ -219,12 +295,16 @@ extern int lammps_get_mpi_comm(void *handle);
extern int lammps_extract_setting(void *handle, const char *keyword);
extern int lammps_extract_global_datatype(void *handle, const char *name);
extern void *lammps_extract_global(void *handle, const char *name);
extern int lammps_extract_atom_datatype(void *handle, const char *name);
extern void *lammps_extract_atom(void *handle, const char *name);
extern void *lammps_extract_compute(void *handle, char *id, int, int);
extern void *lammps_extract_fix(void *handle, char *, int, int, int, int);
extern void *lammps_extract_variable(void *handle, char *, char *);
extern int lammps_extract_variable_datatype(void *handle, const char *name);
extern int lammps_set_variable(void *, char *, char *);
extern void lammps_gather_atoms(void *, char *, int, int, void *);
extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
@ -245,6 +325,7 @@ extern int lammps_find_fix_neighlist(void*, char *, int);
extern int lammps_find_compute_neighlist(void*, char *, int);
extern int lammps_neighlist_num_elements(void*, int);
extern void lammps_neighlist_element_neighbors(void *, int, int, int *, int *, int ** );
extern int lammps_version(void *handle);
extern void lammps_get_os_info(char *buffer, int buf_size);
extern int lammps_config_has_mpi_support();
@ -268,14 +349,20 @@ extern int lammps_id_name(void *, const char *, int, char *buffer, int buf_si
extern int lammps_plugin_count();
extern int lammps_plugin_name(int, char *, char *, int);
/*
extern int lammps_encode_image_flags(int ix, int iy, int iz);
extern void lammps_decode_image_flags(int image, int *flags);
extern int64_t lammps_encode_image_flags(int ix, int iy, int iz);
extern void lammps_decode_image_flags(int64_t image, int *flags);
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
extern void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr);
extern void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng);
extern void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial);
* Have not found a good way to map these functions in a general way.
* So some individual customization for the specific use case and compilation is needed.
*
extern int lammps_encode_image_flags(int ix, int iy, int iz);
extern void lammps_decode_image_flags(int image, int *flags);
extern int64_t lammps_encode_image_flags(int ix, int iy, int iz);
extern void lammps_decode_image_flags(int64_t image, int *flags);
* Supporting the fix external callback mechanism will require extra code specific to the application.
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
extern void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, void *ptr);
* these two functions can only be used from the callback, so we don't support them either
extern void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng);
extern void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial);
*/
extern double **lammps_fix_external_get_force(void *handle, const char *id);
extern void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng);
@ -283,12 +370,12 @@ extern void lammps_fix_external_set_virial_global(void *handle, const char *id
extern void lammps_fix_external_set_vector_length(void *handle, const char *id, int len);
extern void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val);
extern void lammps_flush_buffers(void *ptr);
extern void lammps_free(void *ptr);
extern int lammps_is_running(void *handle);
extern void lammps_force_timeout(void *handle);
extern int lammps_has_error(void *handle);
extern int lammps_get_last_error_message(void *handle, char *buffer, int buf_size);
extern int lammps_python_api_version();
extern void lammps_flush_buffers(void *ptr);
/* last revised on 4 February 2022 */
/* last revised on 3 October 2022 */

27
unittest/c-library/test_library_properties.cpp
View File

@ -434,6 +434,33 @@ TEST_F(LibraryProperties, neighlist)
}
};
TEST_F(LibraryProperties, has_error)
{
// need errors to throw exceptions to be able to intercept them.
if (!lammps_config_has_exceptions()) GTEST_SKIP();
EXPECT_EQ(lammps_has_error(lmp), 0);
// trigger an error, but hide output
::testing::internal::CaptureStdout();
lammps_command(lmp, "this_is_not_a_known_command");
::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_has_error(lmp), 1);
// retrieve error message
char errmsg[1024];
int err = lammps_get_last_error_message(lmp, errmsg, 1024);
EXPECT_EQ(err, 1);
EXPECT_THAT(errmsg, HasSubstr("ERROR: Unknown command: this_is_not_a_known_command"));
// retrieving the error message clear the error status
EXPECT_EQ(lammps_has_error(lmp), 0);
err = lammps_get_last_error_message(lmp, errmsg, 1024);
EXPECT_EQ(err, 0);
EXPECT_THAT(errmsg, StrEq(""));
};
class AtomProperties : public ::testing::Test {
protected:
void *lmp;

23
unittest/fortran/CMakeLists.txt
View File

@ -50,13 +50,34 @@ if(CMAKE_Fortran_COMPILER)
add_test(NAME FortranBox COMMAND test_fortran_box)
add_executable(test_fortran_properties wrap_properties.cpp test_fortran_properties.f90 test_fortran_commands.f90)
target_link_libraries(test_fortran_properties PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
target_link_libraries(test_fortran_properties PRIVATE flammps lammps MPI::MPI_Fortran GTest::GMockMain)
add_test(NAME FortranProperties COMMAND test_fortran_properties)
add_executable(test_fortran_extract_global wrap_extract_global.cpp test_fortran_extract_global.f90)
target_link_libraries(test_fortran_extract_global PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractGlobal COMMAND test_fortran_extract_global)
add_executable(test_fortran_extract_atom wrap_extract_atom.cpp test_fortran_extract_atom.f90)
target_link_libraries(test_fortran_extract_atom PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractAtom COMMAND test_fortran_extract_atom)
add_executable(test_fortran_extract_compute wrap_extract_compute.cpp test_fortran_extract_compute.f90)
target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractCompute COMMAND test_fortran_extract_compute)
add_executable(test_fortran_extract_fix wrap_extract_fix.cpp test_fortran_extract_fix.f90)
target_link_libraries(test_fortran_extract_fix PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractFix COMMAND test_fortran_extract_fix)
add_executable(test_fortran_extract_variable wrap_extract_variable.cpp test_fortran_extract_variable.f90)
target_compile_definitions(test_fortran_extract_variable PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
target_link_libraries(test_fortran_extract_variable PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractVariable COMMAND test_fortran_extract_variable)
add_executable(test_fortran_gather_scatter wrap_gather_scatter.cpp test_fortran_gather_scatter.f90)
target_link_libraries(test_fortran_gather_scatter PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranGatherScatter COMMAND test_fortran_gather_scatter)
else()
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler")
endif()

8
unittest/fortran/atomdata.txt Normal file
View File

@ -0,0 +1,8 @@
3
2 1.6
1 5.2
3 -1.4
2
3 2.5
1 -1.1

9
unittest/fortran/greetings.txt Normal file
View File

@ -0,0 +1,9 @@
hello
god_dag
hola
bonjour
guten_Tag
konnichiwa
shalom
salve
goedendag

14
unittest/fortran/keepstuff.f90
View File

@ -3,24 +3,26 @@ MODULE keepstuff
IMPLICIT NONE
TYPE(LAMMPS) :: lmp
INTEGER :: mycomm
CHARACTER(len=40), DIMENSION(3), PARAMETER :: demo_input = &
[ CHARACTER(len=40) :: &
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: demo_input = &
[ CHARACTER(LEN=40) :: &
'region box block 0 $x 0 2 0 2', &
'create_box 1 box', &
'create_atoms 1 single 1.0 1.0 ${zpos}' ]
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: big_input = &
[ CHARACTER(len=40) :: &
[ CHARACTER(LEN=40) :: &
'region box block 0 $x 0 3 0 4', &
'create_box 1 box', &
'create_atoms 1 single 1.0 1.0 ${zpos}' ]
CHARACTER(len=40), DIMENSION(2), PARAMETER :: cont_input = &
[ CHARACTER(len=40) :: &
CHARACTER(LEN=40), DIMENSION(2), PARAMETER :: cont_input = &
[ CHARACTER(LEN=40) :: &
'create_atoms 1 single &', &
' 0.2 0.1 0.1' ]
CHARACTER(LEN=40), DIMENSION(1), PARAMETER :: more_input = &
[ CHARACTER(LEN=40) :: 'create_atoms 1 single 0.5 0.5 0.5' ]
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: pair_input = &
[ CHARACTER(LEN=40) :: &
'pair_style lj/cut 2.5', &
'pair_coeff 1 1 1.0 1.0', &
'mass 1 1.0' ]
'mass 1 2.0' ]
END MODULE keepstuff

42
unittest/fortran/test_fortran_box.f90
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@ -23,7 +23,7 @@ SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close")
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_box_setup () BIND(C)
SUBROUTINE f_lammps_box_setup() BIND(C)
USE liblammps
USE keepstuff, ONLY : lmp, demo_input
IMPLICIT NONE
@ -39,84 +39,84 @@ SUBROUTINE f_lammps_delete_everything() BIND(C)
CALL lmp%command("delete_atoms group all");
END SUBROUTINE f_lammps_delete_everything
FUNCTION f_lammps_extract_box_xlo () BIND(C)
FUNCTION f_lammps_extract_box_xlo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_xlo
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_xlo
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxlo=boxdim)
f_lammps_extract_box_xlo = boxdim(1)
END FUNCTION f_lammps_extract_box_xlo
FUNCTION f_lammps_extract_box_xhi () BIND(C)
FUNCTION f_lammps_extract_box_xhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_xhi
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_xhi
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxhi=boxdim)
f_lammps_extract_box_xhi = boxdim(1)
END FUNCTION f_lammps_extract_box_xhi
FUNCTION f_lammps_extract_box_ylo () BIND(C)
FUNCTION f_lammps_extract_box_ylo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_ylo
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_ylo
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxlo=boxdim)
f_lammps_extract_box_ylo = boxdim(2)
END FUNCTION f_lammps_extract_box_ylo
FUNCTION f_lammps_extract_box_yhi () BIND(C)
FUNCTION f_lammps_extract_box_yhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_yhi
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_yhi
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxhi=boxdim)
f_lammps_extract_box_yhi = boxdim(2)
END FUNCTION f_lammps_extract_box_yhi
FUNCTION f_lammps_extract_box_zlo () BIND(C)
FUNCTION f_lammps_extract_box_zlo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_zlo
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_zlo
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxlo=boxdim)
f_lammps_extract_box_zlo = boxdim(2)
END FUNCTION f_lammps_extract_box_zlo
FUNCTION f_lammps_extract_box_zhi () BIND(C)
FUNCTION f_lammps_extract_box_zhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_extract_box_zhi
REAL (c_double) :: boxdim(3)
REAL(c_double) :: f_lammps_extract_box_zhi
REAL(c_double) :: boxdim(3)
CALL lmp%extract_box(boxhi=boxdim)
f_lammps_extract_box_zhi = boxdim(2)
END FUNCTION f_lammps_extract_box_zhi
SUBROUTINE f_lammps_reset_box_2x () BIND(C)
SUBROUTINE f_lammps_reset_box_2x() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: newlo(3), newhi(3), xy, yz, xz
REAL(c_double) :: newlo(3), newhi(3), xy, yz, xz
xy = 0.0_c_double
yz = 0.0_c_double

123
unittest/fortran/test_fortran_extract_atom.f90 Normal file
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@ -0,0 +1,123 @@
FUNCTION f_lammps_with_args() BIND(C, name="f_lammps_with_args")
USE ISO_C_BINDING, ONLY: c_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none', &
'-echo','screen','-nocite','-var','zpos','1.5','-var','x','2']
lmp = lammps(args)
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close")
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_atom() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(pair_input)
END SUBROUTINE f_lammps_setup_extract_atom
FUNCTION f_lammps_extract_atom_mass() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_atom_mass
REAL(c_double), DIMENSION(:), POINTER :: mass => NULL()
mass = lmp%extract_atom('mass')
f_lammps_extract_atom_mass = mass(1)
END FUNCTION f_lammps_extract_atom_mass
FUNCTION f_lammps_extract_atom_tag_int(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_extract_atom_tag_int
INTEGER(c_int), DIMENSION(:), POINTER :: tag => NULL()
tag = lmp%extract_atom('id')
f_lammps_extract_atom_tag_int = tag(i)
END FUNCTION f_lammps_extract_atom_tag_int
FUNCTION f_lammps_extract_atom_tag_int64(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int64_t), INTENT(IN), VALUE :: i
INTEGER(c_int64_t) :: f_lammps_extract_atom_tag_int64
INTEGER(c_int64_t), DIMENSION(:), POINTER :: tag => NULL()
tag = lmp%extract_atom('id')
f_lammps_extract_atom_tag_int64 = tag(i)
END FUNCTION f_lammps_extract_atom_tag_int64
FUNCTION f_lammps_extract_atom_type(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_extract_atom_type
INTEGER(c_int), DIMENSION(:), POINTER :: atype => NULL()
atype = lmp%extract_atom('type')
f_lammps_extract_atom_type = atype(i)
END FUNCTION f_lammps_extract_atom_type
FUNCTION f_lammps_extract_atom_mask(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_extract_atom_mask
INTEGER(c_int), DIMENSION(:), POINTER :: mask => NULL()
mask = lmp%extract_atom('mask')
f_lammps_extract_atom_mask = mask(i)
END FUNCTION f_lammps_extract_atom_mask
SUBROUTINE f_lammps_extract_atom_x(i, x) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double), DIMENSION(3) :: x
REAL(c_double), DIMENSION(:,:), POINTER :: xptr => NULL()
xptr = lmp%extract_atom('x')
x = xptr(:,i)
END SUBROUTINE f_lammps_extract_atom_x
SUBROUTINE f_lammps_extract_atom_v(i, v) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double), DIMENSION(3) :: v
REAL(c_double), DIMENSION(:,:), POINTER :: vptr => NULL()
vptr = lmp%extract_atom('v')
v = vptr(:,i)
END SUBROUTINE f_lammps_extract_atom_v

133
unittest/fortran/test_fortran_extract_compute.f90 Normal file
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@ -0,0 +1,133 @@
FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: c_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none', &
'-echo','screen','-nocite','-var','zpos','1.5','-var','x','2']
lmp = lammps(args)
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_compute() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(more_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command("compute peratompe all pe/atom") ! per-atom vector
call lmp%command("compute stress all stress/atom thermo_temp") ! per-atom array
CALL lmp%command("compute totalpe all reduce sum c_peratompe") ! global scalar
CALL lmp%command("compute COM all com") ! global vector
CALL lmp%command("compute RDF all rdf 100") ! global array
CALL lmp%command("compute pairdist all pair/local dist") ! local vector
CALL lmp%command("compute pairlocal all pair/local dist dx dy dz") ! local array
CALL lmp%command("thermo_style custom step pe c_totalpe c_COM[1]")
CALL lmp%command("run 0") ! must be here, otherwise will SEGFAULT
END SUBROUTINE f_lammps_setup_extract_compute
FUNCTION f_lammps_extract_compute_peratom_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_compute_peratom_vector
REAL(c_double), DIMENSION(:), POINTER :: vector => NULL()
vector = lmp%extract_compute('peratompe', lmp%style%atom, lmp%type%vector)
f_lammps_extract_compute_peratom_vector = vector(i)
END FUNCTION f_lammps_extract_compute_peratom_vector
FUNCTION f_lammps_extract_compute_peratom_array(i,j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i, j
REAL(c_double) :: f_lammps_extract_compute_peratom_array
REAL(c_double), DIMENSION(:,:), POINTER :: array => NULL()
array = lmp%extract_compute('stress', lmp%style%atom, lmp%type%array)
f_lammps_extract_compute_peratom_array = array(i,j)
END FUNCTION f_lammps_extract_compute_peratom_array
FUNCTION f_lammps_extract_compute_global_scalar() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_compute_global_scalar
REAL(c_double), POINTER :: scalar
scalar = lmp%extract_compute('totalpe', lmp%style%global, lmp%type%scalar)
f_lammps_extract_compute_global_scalar = scalar
END FUNCTION f_lammps_extract_compute_global_scalar
FUNCTION f_lammps_extract_compute_global_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_compute_global_vector
REAL(c_double), DIMENSION(:), POINTER :: vector
vector = lmp%extract_compute('COM', lmp%style%global, lmp%type%vector)
f_lammps_extract_compute_global_vector = vector(i)
END FUNCTION f_lammps_extract_compute_global_vector
FUNCTION f_lammps_extract_compute_global_array(i,j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i, j
REAL(c_double) :: f_lammps_extract_compute_global_array
REAL(c_double), DIMENSION(:,:), POINTER :: array
array = lmp%extract_compute('RDF', lmp%style%global, lmp%type%array)
f_lammps_extract_compute_global_array = array(i,j)
END FUNCTION f_lammps_extract_compute_global_array
FUNCTION f_lammps_extract_compute_local_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_compute_local_vector
REAL(c_double), DIMENSION(:), POINTER :: vector
vector = lmp%extract_compute('pairdist', lmp%style%local, lmp%type%vector)
f_lammps_extract_compute_local_vector = vector(i)
END FUNCTION f_lammps_extract_compute_local_vector
FUNCTION f_lammps_extract_compute_local_array(i, j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i, j
REAL(c_double) :: f_lammps_extract_compute_local_array
REAL(c_double), DIMENSION(:,:), POINTER :: array
array = lmp%extract_compute('pairlocal', lmp%style%local, lmp%type%array)
f_lammps_extract_compute_local_array = array(i,j)
END FUNCTION f_lammps_extract_compute_local_array

99
unittest/fortran/test_fortran_extract_fix.f90 Normal file
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@ -0,0 +1,99 @@
FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: C_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(C_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none', &
'-echo','screen','-nocite','-var','zpos','1.5','-var','x','2']
lmp = lammps(args)
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = C_NULL_PTR
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_fix() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input, more_input
IMPLICIT NONE
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(more_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command("fix state all store/state 0 z") ! per-atom vector
CALL lmp%command("fix move all move linear 0 0 0") ! for per-atom array
CALL lmp%command("fix recenter all recenter 1 1 1") ! global scalar, vector
CALL lmp%command("variable natoms equal count(all)")
CALL lmp%command("variable ts equal step")
CALL lmp%command("fix vec all vector 1 v_natoms v_ts") ! global array
CALL lmp%command("run 1") ! must be 1, otherwise move/recenter won't happen
END SUBROUTINE f_lammps_setup_extract_fix
FUNCTION f_lammps_extract_fix_global_scalar() BIND(C) RESULT(scalar)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: scalar
scalar = lmp%extract_fix("recenter", lmp%style%global, lmp%type%scalar)
END FUNCTION f_lammps_extract_fix_global_scalar
FUNCTION f_lammps_extract_fix_global_vector(i) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: element
element = lmp%extract_fix("recenter", lmp%style%global, lmp%type%vector, i)
END FUNCTION f_lammps_extract_fix_global_vector
FUNCTION f_lammps_extract_fix_global_array(i,j) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i, j
REAL(c_double) :: element
element = lmp%extract_fix("vec", lmp%style%global, lmp%type%array, i, j)
END FUNCTION f_lammps_extract_fix_global_array
FUNCTION f_lammps_extract_fix_peratom_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_fix_peratom_vector
REAL(c_double), DIMENSION(:), POINTER :: vector
vector = lmp%extract_fix("state", lmp%style%atom, lmp%type%vector, -1, -1)
f_lammps_extract_fix_peratom_vector = vector(i)
END FUNCTION f_lammps_extract_fix_peratom_vector
FUNCTION f_lammps_extract_fix_peratom_array(i,j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i, j
REAL(c_double) :: f_lammps_extract_fix_peratom_array
REAL(c_double), DIMENSION(:,:), POINTER :: array
array = lmp%extract_fix("move", lmp%style%atom, lmp%type%array, -1, -1)
f_lammps_extract_fix_peratom_array = array(i,j)
END FUNCTION f_lammps_extract_fix_peratom_array

298
unittest/fortran/test_fortran_extract_global.f90
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@ -22,7 +22,7 @@ SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close")
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_global () BIND(C)
SUBROUTINE f_lammps_setup_extract_global() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
IMPLICIT NONE
@ -33,12 +33,12 @@ SUBROUTINE f_lammps_setup_extract_global () BIND(C)
CALL lmp%command('run 0')
END SUBROUTINE f_lammps_setup_extract_global
SUBROUTINE f_lammps_setup_full_extract_global () BIND(C)
SUBROUTINE f_lammps_setup_full_extract_global() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTERFACE
SUBROUTINE f_lammps_setup_extract_global () BIND(C)
SUBROUTINE f_lammps_setup_extract_global() BIND(C)
END SUBROUTINE f_lammps_setup_extract_global
END INTERFACE
@ -50,422 +50,428 @@ SUBROUTINE f_lammps_setup_full_extract_global () BIND(C)
CALL lmp%command('run 0')
END SUBROUTINE f_lammps_setup_full_extract_global
FUNCTION f_lammps_extract_global_units () BIND(C) RESULT(success)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_units() BIND(C) RESULT(success)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER (C_int) :: success
CHARACTER (LEN=16) :: units
INTEGER(c_int) :: success
CHARACTER(LEN=16) :: units
! passing strings from Fortran to C is icky, so we do the test here and
! report the result instead
units = lmp%extract_global('units')
IF ( TRIM(units) == 'lj' ) THEN
success = 1_C_int
IF (TRIM(units) == 'lj') THEN
success = 1_c_int
ELSE
success = 0_C_int
success = 0_c_int
END IF
END FUNCTION f_lammps_extract_global_units
FUNCTION f_lammps_extract_global_ntimestep () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_ntimestep() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: ntimestep
INTEGER (C_int) :: f_lammps_extract_global_ntimestep
INTEGER(c_int), POINTER :: ntimestep
INTEGER(c_int) :: f_lammps_extract_global_ntimestep
ntimestep = lmp%extract_global("ntimestep")
f_lammps_extract_global_ntimestep = ntimestep
END FUNCTION f_lammps_extract_global_ntimestep
FUNCTION f_lammps_extract_global_ntimestep_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_ntimestep_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: ntimestep
INTEGER (C_int64_t) :: f_lammps_extract_global_ntimestep_big
INTEGER(c_int64_t), POINTER :: ntimestep
INTEGER(c_int64_t) :: f_lammps_extract_global_ntimestep_big
ntimestep = lmp%extract_global("ntimestep")
f_lammps_extract_global_ntimestep_big = ntimestep
END FUNCTION f_lammps_extract_global_ntimestep_big
FUNCTION f_lammps_extract_global_dt () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_dt() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double), POINTER :: dt
REAL (C_double) :: f_lammps_extract_global_dt
REAL(c_double), POINTER :: dt
REAL(c_double) :: f_lammps_extract_global_dt
dt = lmp%extract_global("dt")
f_lammps_extract_global_dt = dt
END FUNCTION f_lammps_extract_global_dt
SUBROUTINE f_lammps_extract_global_boxlo (C_boxlo) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
SUBROUTINE f_lammps_extract_global_boxlo(C_boxlo) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double), DIMENSION(3) :: C_boxlo
REAL (C_double), DIMENSION(:), POINTER :: boxlo
REAL(c_double), DIMENSION(3) :: C_boxlo
REAL(c_double), DIMENSION(:), POINTER :: boxlo
boxlo = lmp%extract_global("boxlo")
C_boxlo = boxlo
END SUBROUTINE f_lammps_extract_global_boxlo
SUBROUTINE f_lammps_extract_global_boxhi (C_boxhi) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
SUBROUTINE f_lammps_extract_global_boxhi(C_boxhi) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double), DIMENSION(3) :: C_boxhi
REAL (C_double), DIMENSION(:), POINTER :: boxhi
REAL(c_double), DIMENSION(3) :: C_boxhi
REAL(c_double), DIMENSION(:), POINTER :: boxhi
boxhi = lmp%extract_global("boxhi")
C_boxhi = boxhi
END SUBROUTINE f_lammps_extract_global_boxhi
FUNCTION f_lammps_extract_global_boxxlo () BIND(C) RESULT(C_boxxlo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxxlo() BIND(C) RESULT(C_boxxlo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxxlo
REAL (C_double), POINTER :: boxxlo
REAL(c_double) :: C_boxxlo
REAL(c_double), POINTER :: boxxlo
boxxlo = lmp%extract_global("boxxlo")
C_boxxlo = boxxlo
END FUNCTION f_lammps_extract_global_boxxlo
FUNCTION f_lammps_extract_global_boxxhi () BIND(C) RESULT(C_boxxhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxxhi() BIND(C) RESULT(C_boxxhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxxhi
REAL (C_double), POINTER :: boxxhi
REAL(c_double) :: C_boxxhi
REAL(c_double), POINTER :: boxxhi
boxxhi = lmp%extract_global("boxxhi")
C_boxxhi = boxxhi
END FUNCTION f_lammps_extract_global_boxxhi
FUNCTION f_lammps_extract_global_boxylo () BIND(C) RESULT(C_boxylo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxylo() BIND(C) RESULT(C_boxylo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxylo
REAL (C_double), POINTER :: boxylo
REAL(c_double) :: C_boxylo
REAL(c_double), POINTER :: boxylo
boxylo = lmp%extract_global("boxylo")
C_boxylo = boxylo
END FUNCTION f_lammps_extract_global_boxylo
FUNCTION f_lammps_extract_global_boxyhi () BIND(C) RESULT(C_boxyhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxyhi() BIND(C) RESULT(C_boxyhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxyhi
REAL (C_double), POINTER :: boxyhi
REAL(c_double) :: C_boxyhi
REAL(c_double), POINTER :: boxyhi
boxyhi = lmp%extract_global("boxyhi")
C_boxyhi = boxyhi
END FUNCTION f_lammps_extract_global_boxyhi
FUNCTION f_lammps_extract_global_boxzlo () BIND(C) RESULT(C_boxzlo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxzlo() BIND(C) RESULT(C_boxzlo)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxzlo
REAL (C_double), POINTER :: boxzlo
REAL(c_double) :: C_boxzlo
REAL(c_double), POINTER :: boxzlo
boxzlo = lmp%extract_global("boxzlo")
C_boxzlo = boxzlo
END FUNCTION f_lammps_extract_global_boxzlo
FUNCTION f_lammps_extract_global_boxzhi () BIND(C) RESULT(C_boxzhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boxzhi() BIND(C) RESULT(C_boxzhi)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_boxzhi
REAL (C_double), POINTER :: boxzhi
REAL(c_double) :: C_boxzhi
REAL(c_double), POINTER :: boxzhi
boxzhi = lmp%extract_global("boxzhi")
C_boxzhi = boxzhi
END FUNCTION f_lammps_extract_global_boxzhi
SUBROUTINE f_lammps_extract_global_periodicity (C_periodicity) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
SUBROUTINE f_lammps_extract_global_periodicity(C_periodicity) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), DIMENSION(3) :: C_periodicity
INTEGER (C_int), DIMENSION(:), POINTER :: periodicity
INTEGER(c_int), DIMENSION(3) :: C_periodicity
INTEGER(c_int), DIMENSION(:), POINTER :: periodicity
periodicity = lmp%extract_global("periodicity")
C_periodicity = periodicity
END SUBROUTINE f_lammps_extract_global_periodicity
FUNCTION f_lammps_extract_global_triclinic () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_triclinic() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: triclinic
INTEGER (C_int) :: f_lammps_extract_global_triclinic
INTEGER(c_int), POINTER :: triclinic
INTEGER(c_int) :: f_lammps_extract_global_triclinic
triclinic = lmp%extract_global("triclinic")
f_lammps_extract_global_triclinic = triclinic
END FUNCTION f_lammps_extract_global_triclinic
FUNCTION f_lammps_extract_global_xy () BIND(C) RESULT(C_xy)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_xy() BIND(C) RESULT(C_xy)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_xy
REAL (C_double), POINTER :: xy
REAL(c_double) :: C_xy
REAL(c_double), POINTER :: xy
xy = lmp%extract_global("xy")
C_xy = xy
END FUNCTION f_lammps_extract_global_xy
FUNCTION f_lammps_extract_global_xz () BIND(C) RESULT(C_xz)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_xz() BIND(C) RESULT(C_xz)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_xz
REAL (C_double), POINTER :: xz
REAL(c_double) :: C_xz
REAL(c_double), POINTER :: xz
xz = lmp%extract_global("xz")
C_xz = xz
END FUNCTION f_lammps_extract_global_xz
FUNCTION f_lammps_extract_global_yz () BIND(C) RESULT(C_yz)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_yz() BIND(C) RESULT(C_yz)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_yz
REAL (C_double), POINTER :: yz
REAL(c_double) :: C_yz
REAL(c_double), POINTER :: yz
yz = lmp%extract_global("yz")
C_yz = yz
END FUNCTION f_lammps_extract_global_yz
FUNCTION f_lammps_extract_global_natoms () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_natoms() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: natoms
INTEGER (C_int) :: f_lammps_extract_global_natoms
INTEGER(c_int), POINTER :: natoms
INTEGER(c_int) :: f_lammps_extract_global_natoms
natoms = lmp%extract_global("natoms")
f_lammps_extract_global_natoms = natoms
END FUNCTION f_lammps_extract_global_natoms
FUNCTION f_lammps_extract_global_natoms_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_natoms_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: natoms
INTEGER (C_int64_t) :: f_lammps_extract_global_natoms_big
INTEGER(c_int64_t), POINTER :: natoms
INTEGER(c_int64_t) :: f_lammps_extract_global_natoms_big
natoms = lmp%extract_global("natoms")
f_lammps_extract_global_natoms_big = natoms
END FUNCTION f_lammps_extract_global_natoms_big
FUNCTION f_lammps_extract_global_nbonds () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nbonds() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nbonds
INTEGER (C_int) :: f_lammps_extract_global_nbonds
INTEGER(c_int), POINTER :: nbonds
INTEGER(c_int) :: f_lammps_extract_global_nbonds
nbonds = lmp%extract_global("nbonds")
f_lammps_extract_global_nbonds = nbonds
END FUNCTION f_lammps_extract_global_nbonds
FUNCTION f_lammps_extract_global_nbonds_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_nbonds_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: nbonds
INTEGER (C_int64_t) :: f_lammps_extract_global_nbonds_big
INTEGER(c_int64_t), POINTER :: nbonds
INTEGER(c_int64_t) :: f_lammps_extract_global_nbonds_big
nbonds = lmp%extract_global("nbonds")
f_lammps_extract_global_nbonds_big = nbonds
END FUNCTION f_lammps_extract_global_nbonds_big
FUNCTION f_lammps_extract_global_nangles () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nangles() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nangles
INTEGER (C_int) :: f_lammps_extract_global_nangles
INTEGER(c_int), POINTER :: nangles
INTEGER(c_int) :: f_lammps_extract_global_nangles
nangles = lmp%extract_global("nangles")
f_lammps_extract_global_nangles = nangles
END FUNCTION f_lammps_extract_global_nangles
FUNCTION f_lammps_extract_global_nangles_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_nangles_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: nangles
INTEGER (C_int64_t) :: f_lammps_extract_global_nangles_big
INTEGER(c_int64_t), POINTER :: nangles
INTEGER(c_int64_t) :: f_lammps_extract_global_nangles_big
nangles = lmp%extract_global("nangles")
f_lammps_extract_global_nangles_big = nangles
END FUNCTION f_lammps_extract_global_nangles_big
FUNCTION f_lammps_extract_global_ndihedrals () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_ndihedrals() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: ndihedrals
INTEGER (C_int) :: f_lammps_extract_global_ndihedrals
INTEGER(c_int), POINTER :: ndihedrals
INTEGER(c_int) :: f_lammps_extract_global_ndihedrals
ndihedrals = lmp%extract_global("ndihedrals")
f_lammps_extract_global_ndihedrals = ndihedrals
END FUNCTION f_lammps_extract_global_ndihedrals
FUNCTION f_lammps_extract_global_ndihedrals_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_ndihedrals_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: ndihedrals
INTEGER (C_int64_t) :: f_lammps_extract_global_ndihedrals_big
INTEGER(c_int64_t), POINTER :: ndihedrals
INTEGER(c_int64_t) :: f_lammps_extract_global_ndihedrals_big
ndihedrals = lmp%extract_global("ndihedrals")
f_lammps_extract_global_ndihedrals_big = ndihedrals
END FUNCTION f_lammps_extract_global_ndihedrals_big
FUNCTION f_lammps_extract_global_nimpropers () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nimpropers() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nimpropers
INTEGER (C_int) :: f_lammps_extract_global_nimpropers
INTEGER(c_int), POINTER :: nimpropers
INTEGER(c_int) :: f_lammps_extract_global_nimpropers
nimpropers = lmp%extract_global("nimpropers")
f_lammps_extract_global_nimpropers = nimpropers
END FUNCTION f_lammps_extract_global_nimpropers
FUNCTION f_lammps_extract_global_nimpropers_big () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
FUNCTION f_lammps_extract_global_nimpropers_big() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int64_t), POINTER :: nimpropers
INTEGER (C_int64_t) :: f_lammps_extract_global_nimpropers_big
INTEGER(c_int64_t), POINTER :: nimpropers
INTEGER(c_int64_t) :: f_lammps_extract_global_nimpropers_big
nimpropers = lmp%extract_global("nimpropers")
f_lammps_extract_global_nimpropers_big = nimpropers
END FUNCTION f_lammps_extract_global_nimpropers_big
FUNCTION f_lammps_extract_global_ntypes () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_ntypes() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: ntypes
INTEGER (C_int) :: f_lammps_extract_global_ntypes
INTEGER(c_int), POINTER :: ntypes
INTEGER(c_int) :: f_lammps_extract_global_ntypes
ntypes = lmp%extract_global("ntypes")
f_lammps_extract_global_ntypes = ntypes
END FUNCTION f_lammps_extract_global_ntypes
FUNCTION f_lammps_extract_global_nlocal () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nlocal() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nlocal
INTEGER (C_int) :: f_lammps_extract_global_nlocal
INTEGER(c_int), POINTER :: nlocal
INTEGER(c_int) :: f_lammps_extract_global_nlocal
nlocal = lmp%extract_global("nlocal")
f_lammps_extract_global_nlocal = nlocal
END FUNCTION f_lammps_extract_global_nlocal
FUNCTION f_lammps_extract_global_nghost () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nghost() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nghost
INTEGER (C_int) :: f_lammps_extract_global_nghost
INTEGER(c_int), POINTER :: nghost
INTEGER(c_int) :: f_lammps_extract_global_nghost
nghost = lmp%extract_global("nghost")
f_lammps_extract_global_nghost = nghost
END FUNCTION f_lammps_extract_global_nghost
FUNCTION f_lammps_extract_global_nmax () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_extract_global_nmax() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int), POINTER :: nmax
INTEGER (C_int) :: f_lammps_extract_global_nmax
INTEGER(c_int), POINTER :: nmax
INTEGER(c_int) :: f_lammps_extract_global_nmax
nmax = lmp%extract_global("nmax")
f_lammps_extract_global_nmax = nmax
END FUNCTION f_lammps_extract_global_nmax
FUNCTION f_lammps_extract_global_boltz () BIND(C) RESULT(C_k_B)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_boltz() BIND(C) RESULT(C_k_B)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_k_B
REAL (C_double), POINTER :: k_B
REAL(c_double) :: C_k_B
REAL(c_double), POINTER :: k_B
k_B = lmp%extract_global("boltz")
C_k_B = k_B
END FUNCTION f_lammps_extract_global_boltz
FUNCTION f_lammps_extract_global_hplanck () BIND(C) RESULT(C_h)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_hplanck() BIND(C) RESULT(C_h)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: C_h
REAL (C_double), POINTER :: h
REAL(c_double) :: C_h
REAL(c_double), POINTER :: h
h = lmp%extract_global("boltz")
C_h = h
END FUNCTION f_lammps_extract_global_hplanck
FUNCTION f_lammps_extract_global_angstrom () BIND(C) RESULT(Angstrom)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_angstrom() BIND(C) RESULT(Angstrom)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: Angstrom
REAL (C_double), POINTER :: A
REAL(c_double) :: Angstrom
REAL(c_double), POINTER :: A
A = lmp%extract_global("angstrom")
Angstrom = A
END FUNCTION f_lammps_extract_global_angstrom
FUNCTION f_lammps_extract_global_femtosecond () BIND(C) RESULT(fs)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
FUNCTION f_lammps_extract_global_femtosecond() BIND(C) RESULT(fs)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
REAL (C_double) :: fs
REAL (C_double), POINTER :: femtosecond
REAL(c_double) :: fs
REAL(c_double), POINTER :: femtosecond
femtosecond = lmp%extract_global("femtosecond")
fs = femtosecond

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MODULE keepvar
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_size_t, c_char
USE liblammps
IMPLICIT NONE
INTERFACE
FUNCTION c_path_join(a, b) BIND(C)
IMPORT :: c_ptr
TYPE(c_ptr), VALUE :: a, b
TYPE(c_ptr) :: c_path_join
END FUNCTION c_path_join
FUNCTION c_strlen(str) BIND(C,name='strlen')
IMPORT :: c_ptr, c_size_t
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: str
INTEGER(c_size_t) :: c_strlen
END FUNCTION c_strlen
SUBROUTINE c_free(ptr) BIND(C,name='free')
IMPORT :: c_ptr
TYPE(c_ptr), VALUE :: ptr
END SUBROUTINE c_free
END INTERFACE
CONTAINS
FUNCTION absolute_path(filename)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_size_t, c_char, C_F_POINTER
USE keepstuff, ONLY : lmp
CHARACTER(LEN=:), ALLOCATABLE :: absolute_path
CHARACTER(LEN=*), INTENT(IN) :: filename
CHARACTER(LEN=256) :: test_input_directory
TYPE(c_ptr) :: c_test_input_directory, c_absolute_path, c_filename
CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: F_absolute_path
INTEGER(c_size_t) :: i, length
test_input_directory = lmp%extract_variable('input_dir')
c_test_input_directory = f2c_string(test_input_directory)
c_filename = f2c_string(filename)
c_absolute_path = c_path_join(c_test_input_directory, c_filename)
length = c_strlen(c_absolute_path)
CALL C_F_POINTER(c_absolute_path, F_absolute_path, [length])
ALLOCATE(CHARACTER(LEN=length) :: absolute_path)
DO i = 1, length
absolute_path(i:i) = F_absolute_path(i)
END DO
CALL c_free(c_filename)
CALL c_free(c_test_input_directory)
CALL c_free(c_absolute_path)
END FUNCTION absolute_path
FUNCTION f2c_string(f_string) RESULT(ptr)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_char, c_ptr, c_size_t, &
c_null_char, C_F_POINTER
CHARACTER(LEN=*), INTENT(IN) :: f_string
CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:)
TYPE(c_ptr) :: ptr
INTEGER(c_size_t) :: i, n
INTERFACE
FUNCTION lammps_malloc(size) BIND(C, name='malloc')
IMPORT :: c_ptr, c_size_t
IMPLICIT NONE
INTEGER(c_size_t), VALUE :: size
TYPE(c_ptr) :: lammps_malloc
END FUNCTION lammps_malloc
END INTERFACE
n = LEN_TRIM(f_string)
ptr = lammps_malloc(n+1)
CALL C_F_POINTER(ptr, c_string, [1])
DO i=1, n
c_string(i) = f_string(i:i)
END DO
c_string(n+1) = c_null_char
END FUNCTION f2c_string
END MODULE keepvar
FUNCTION f_lammps_with_C_args(argc, argv) BIND(C)
USE ISO_C_BINDING, ONLY: c_ptr, c_char, c_int, c_size_t, C_F_POINTER
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: argc
TYPE(c_ptr), VALUE :: argv
TYPE(c_ptr), DIMENSION(:), POINTER :: Fargv
INTEGER, PARAMETER :: ARG_LENGTH = 256
TYPE(c_ptr) :: f_lammps_with_C_args
CHARACTER(LEN=ARG_LENGTH), DIMENSION(argc) :: args
CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Cstr
INTEGER(c_size_t):: i, length, j
INTERFACE
FUNCTION c_strlen(str) BIND(C,name='strlen')
IMPORT :: c_ptr, c_size_t
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: str
INTEGER(c_size_t) :: c_strlen
END FUNCTION c_strlen
END INTERFACE
CALL C_F_POINTER(argv, Fargv, [argc])
DO i = 1, argc
args(i) = ''
length = c_strlen(Fargv(i))
CALL C_F_POINTER(Fargv(i), Cstr, [length])
DO j = 1, length
args(i)(j:j) = Cstr(j)
END DO
END DO
lmp = lammps(args)
f_lammps_with_C_args = lmp%handle
END FUNCTION f_lammps_with_C_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_variable() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input, pair_input
USE keepvar, ONLY : absolute_path
IMPLICIT NONE
! Had to do this one as one string because lammps_commands_list and
! lammps_commands_string do not play well with triple quotes
CHARACTER(LEN=256), PARAMETER :: py_input = &
'python square_it input 1 v_lp return v_py format ff here """' &
// NEW_LINE(' ') // 'def square_it(N) :' &
// NEW_LINE(' ') // ' return N*N' &
// NEW_LINE(' ') // '"""'
CALL lmp%command('atom_modify map array')
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(more_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command('variable idx index "hello" "goodbye"')
CALL lmp%command('variable lp loop 10')
CALL lmp%command('variable lp_pad loop 10 pad')
CALL lmp%command('variable wld world "group1"')
CALL lmp%command('variable uni universe "universe1" "universeA"')
CALL lmp%command('variable ulp uloop 2')
CALL lmp%command('variable str string "this is a string"')
CALL lmp%command('variable ex equal exp(v_lp)')
CALL lmp%command('variable fmt format ex %.6G')
CALL lmp%command('variable fmt_pad format ex %08.6g')
CALL lmp%command('variable username getenv FORTRAN_USER')
CALL lmp%command('variable greeting file ' // absolute_path('greetings.txt'))
CALL lmp%command('variable atfile atomfile ' &
// absolute_path('atomdata.txt'))
IF (lmp%config_has_package('PYTHON')) THEN
CALL lmp%command(py_input)
CALL lmp%command('variable py python square_it')
END IF
CALL lmp%command('variable time timer')
CALL lmp%command('variable int internal 4')
CALL lmp%command('variable at_z atom z')
CALL lmp%command("compute COM all com") ! defines a global vector
CALL lmp%command("variable center vector c_COM")
! make sure COM is computable...
CALL lmp%command("thermo_style custom step pe c_COM[1] v_center[1]")
CALL lmp%command("run 0") ! so c_COM and v_center have values
END SUBROUTINE f_lammps_setup_extract_variable
FUNCTION f_lammps_extract_variable_index_1() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_1
CHARACTER(LEN=256) :: str
str = lmp%extract_variable("idx")
IF (trim(str) == 'hello') THEN
f_lammps_extract_variable_index_1 = 1_c_int
ELSE
f_lammps_extract_variable_index_1 = 0_c_int
END IF
END FUNCTION f_lammps_extract_variable_index_1
FUNCTION f_lammps_extract_variable_index_2() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_2
CHARACTER(LEN=256) :: str
str = lmp%extract_variable("idx")
IF (trim(str) == 'goodbye') THEN
f_lammps_extract_variable_index_2 = 1_c_int
ELSE
f_lammps_extract_variable_index_2 = 0_c_int
END IF
END FUNCTION f_lammps_extract_variable_index_2
FUNCTION f_lammps_extract_variable_loop() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_loop
CHARACTER(LEN=256) :: loop
loop = lmp%extract_variable('lp')
READ(loop,*) f_lammps_extract_variable_loop
END FUNCTION f_lammps_extract_variable_loop
FUNCTION f_lammps_extract_variable_loop_pad() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_loop_pad
CHARACTER(LEN=20) :: loop
loop = lmp%extract_variable('lp_pad')
f_lammps_extract_variable_loop_pad = f2c_string(loop)
END FUNCTION f_lammps_extract_variable_loop_pad
FUNCTION f_lammps_extract_variable_world() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_world
CHARACTER(LEN=20) :: world
world = lmp%extract_variable('wld')
f_lammps_extract_variable_world = f2c_string(world)
END FUNCTION f_lammps_extract_variable_world
FUNCTION f_lammps_extract_variable_universe() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_universe
CHARACTER(LEN=20) :: universe
universe = lmp%extract_variable('uni')
f_lammps_extract_variable_universe = f2c_string(universe)
END FUNCTION f_lammps_extract_variable_universe
FUNCTION f_lammps_extract_variable_uloop() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_uloop
CHARACTER(LEN=256) :: uloop
uloop = lmp%extract_variable('ulp')
READ(uloop,*) f_lammps_extract_variable_uloop
END FUNCTION f_lammps_extract_variable_uloop
FUNCTION f_lammps_extract_variable_string() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_string
CHARACTER(LEN=256) :: string
string = lmp%extract_variable('str')
f_lammps_extract_variable_string = f2c_string(string)
END FUNCTION f_lammps_extract_variable_string
FUNCTION f_lammps_extract_variable_format() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_format
CHARACTER(LEN=20) :: form
form = lmp%extract_variable('fmt')
f_lammps_extract_variable_format = f2c_string(form)
END FUNCTION f_lammps_extract_variable_format
FUNCTION f_lammps_extract_variable_format_pad() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_format_pad
CHARACTER(LEN=20) :: form
form = lmp%extract_variable('fmt_pad')
f_lammps_extract_variable_format_pad = f2c_string(form)
END FUNCTION f_lammps_extract_variable_format_pad
FUNCTION f_lammps_extract_variable_getenv() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_getenv
CHARACTER(LEN=40) :: string
string = lmp%extract_variable('username')
f_lammps_extract_variable_getenv = f2c_string(string)
END FUNCTION f_lammps_extract_variable_getenv
FUNCTION f_lammps_extract_variable_file() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_file
CHARACTER(LEN=40) :: string
string = lmp%extract_variable('greeting')
f_lammps_extract_variable_file = f2c_string(string)
END FUNCTION f_lammps_extract_variable_file
FUNCTION f_lammps_extract_variable_atomfile(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_atomfile
REAL(c_double), DIMENSION(:), ALLOCATABLE :: atom_data
atom_data = lmp%extract_variable('atfile')
f_lammps_extract_variable_atomfile = atom_data(i)
END FUNCTION f_lammps_extract_variable_atomfile
FUNCTION f_lammps_extract_variable_python() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_python
f_lammps_extract_variable_python = lmp%extract_variable('py')
END FUNCTION f_lammps_extract_variable_python
FUNCTION f_lammps_extract_variable_timer() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_timer
f_lammps_extract_variable_timer = lmp%extract_variable('time')
END FUNCTION f_lammps_extract_variable_timer
FUNCTION f_lammps_extract_variable_internal() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_internal
f_lammps_extract_variable_internal = lmp%extract_variable('int')
END FUNCTION f_lammps_extract_variable_internal
FUNCTION f_lammps_extract_variable_equal() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_equal
f_lammps_extract_variable_equal = lmp%extract_variable('ex')
END FUNCTION f_lammps_extract_variable_equal
FUNCTION f_lammps_extract_variable_atom(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_atom
REAL(c_double), DIMENSION(:), ALLOCATABLE :: atom
atom = lmp%extract_variable('at_z') ! z-coordinates
f_lammps_extract_variable_atom = atom(i)
END FUNCTION f_lammps_extract_variable_atom
FUNCTION f_lammps_extract_variable_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_vector
REAL(c_double), DIMENSION(:), ALLOCATABLE :: vector
vector = lmp%extract_variable('center') ! z-coordinates
f_lammps_extract_variable_vector = vector(i)
END FUNCTION f_lammps_extract_variable_vector
SUBROUTINE f_lammps_set_variable_string() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
CHARACTER(LEN=40) :: string
string = "this is the new string"
CALL lmp%set_variable('str', string)
END SUBROUTINE f_lammps_set_variable_string
! vim: sts=2 ts=2 sw=2 et

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FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: c_ptr
USE LIBLAMMPS
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none', &
'-echo','screen','-nocite','-var','zpos','1.5','-var','x','2']
lmp = lammps(args)
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_gather_scatter() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input
IMPLICIT NONE
CALL lmp%command('atom_modify map array')
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(more_input)
END SUBROUTINE f_lammps_setup_gather_scatter
FUNCTION f_lammps_gather_atoms_mask(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_gather_atoms_mask
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: mask
CALL lmp%gather_atoms('mask', 1_c_int, mask)
f_lammps_gather_atoms_mask = mask(i)
END FUNCTION f_lammps_gather_atoms_mask
FUNCTION f_lammps_gather_atoms_position(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_gather_atoms_position
REAL(c_double), DIMENSION(:), ALLOCATABLE :: positions
CALL lmp%gather_atoms('x', 3_c_int, positions)
f_lammps_gather_atoms_position = positions(i)
END FUNCTION f_lammps_gather_atoms_position
FUNCTION f_lammps_gather_atoms_concat_mask(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_gather_atoms_concat_mask
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: mask, tag
INTEGER :: j
CALL lmp%gather_atoms_concat('mask', 1_c_int, mask)
CALL lmp%gather_atoms_concat('id', 1_c_int, tag)
DO j = 1, SIZE(tag)
IF (tag(j) == i) THEN
f_lammps_gather_atoms_concat_mask = mask(j)
RETURN
END IF
END DO
f_lammps_gather_atoms_concat_mask = -1
END FUNCTION f_lammps_gather_atoms_concat_mask
FUNCTION f_lammps_gather_atoms_concat_position(xyz, id) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: id, xyz
REAL(c_double) :: f_lammps_gather_atoms_concat_position
REAL(c_double), DIMENSION(:), ALLOCATABLE :: positions
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: tag
INTEGER :: j
CALL lmp%gather_atoms_concat('x', 3_c_int, positions)
CALL lmp%gather_atoms_concat('id', 1_c_int, tag)
DO j = 1, SIZE(tag)
IF (tag(j) == id) THEN
f_lammps_gather_atoms_concat_position = positions((j-1)*3 + xyz)
END IF
END DO
END FUNCTION f_lammps_gather_atoms_concat_position
FUNCTION f_lammps_gather_atoms_subset_mask(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
INTEGER(c_int) :: f_lammps_gather_atoms_subset_mask
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: mask
INTEGER :: j
INTEGER(c_int), DIMENSION(*), PARAMETER :: tag = [3,2]
CALL lmp%gather_atoms_subset('mask', 1_c_int, tag, mask)
DO j = 1, SIZE(tag)
IF (tag(j) == i) THEN
f_lammps_gather_atoms_subset_mask = mask(j)
RETURN
END IF
END DO
f_lammps_gather_atoms_subset_mask = -1
END FUNCTION f_lammps_gather_atoms_subset_mask
FUNCTION f_lammps_gather_atoms_subset_position(xyz,id) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: id, xyz
REAL(c_double) :: f_lammps_gather_atoms_subset_position
REAL(c_double), DIMENSION(:), ALLOCATABLE :: positions
INTEGER(c_int), DIMENSION(*), PARAMETER :: tag = [3,2]
INTEGER :: j
CALL lmp%gather_atoms_subset('x', 3_c_int, tag, positions)
DO j = 1, SIZE(tag)
IF (tag(j) == id) THEN
f_lammps_gather_atoms_subset_position = positions((j-1)*3 + xyz)
RETURN
END IF
END DO
f_lammps_gather_atoms_subset_position = -1.0D0
END FUNCTION f_lammps_gather_atoms_subset_position
SUBROUTINE f_lammps_scatter_atoms_masks() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: masks
INTEGER(c_int) :: swap
CALL lmp%gather_atoms('mask', 1_c_int, masks)
! swap masks of atoms 1 and 3
swap=masks(1)
masks(1) = masks(3)
masks(3) = swap
CALL lmp%scatter_atoms('mask', masks) ! push the swap back to LAMMPS
END SUBROUTINE f_lammps_scatter_atoms_masks
SUBROUTINE f_lammps_scatter_atoms_positions() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: tags
REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET :: xvec
REAL(c_double), DIMENSION(:,:), POINTER :: x
REAL(c_double) :: swap(3)
CALL lmp%gather_atoms('id',1_c_int,tags)
CALL lmp%gather_atoms('x',3_c_int,xvec)
x(1:3,1:SIZE(xvec)/3) => xvec
! swap positions of atoms 1 and 3
swap=x(:,1)
x(:,1) = x(:,3)
x(:,3) = swap
CALL lmp%scatter_atoms('x', xvec) ! push the swap back to LAMMPS
END SUBROUTINE f_lammps_scatter_atoms_positions
SUBROUTINE f_lammps_scatter_atoms_subset_mask() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: all_masks
INTEGER(c_int), DIMENSION(*), PARAMETER :: tags = [3,1]
INTEGER(c_int), DIMENSION(2) :: masks
CALL lmp%gather_atoms('mask', 1_c_int, all_masks)
! swap masks of atoms 1 and 3 in the new array (because 'tags' is reversed)
masks(1) = all_masks(1)
masks(2) = all_masks(3)
CALL lmp%scatter_atoms_subset('mask', tags, masks) ! push the swap to LAMMPS
END SUBROUTINE f_lammps_scatter_atoms_subset_mask

50
unittest/fortran/test_fortran_get_thermo.f90
View File

@ -23,7 +23,7 @@ SUBROUTINE f_lammps_close() BIND(C)
lmp%handle = c_null_ptr
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_get_thermo_setup () BIND(C)
SUBROUTINE f_lammps_get_thermo_setup() BIND(C)
USE liblammps
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
IMPLICIT NONE
@ -33,122 +33,122 @@ SUBROUTINE f_lammps_get_thermo_setup () BIND(C)
CALL lmp%commands_list(pair_input)
END SUBROUTINE f_lammps_get_thermo_setup
FUNCTION f_lammps_get_thermo_natoms () BIND(C)
FUNCTION f_lammps_get_thermo_natoms() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_natoms
REAL(c_double) :: f_lammps_get_thermo_natoms
f_lammps_get_thermo_natoms = lmp%get_thermo('atoms')
END FUNCTION f_lammps_get_thermo_natoms
FUNCTION f_lammps_get_thermo_dt () BIND (C)
FUNCTION f_lammps_get_thermo_dt() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_dt
REAL(c_double) :: f_lammps_get_thermo_dt
f_lammps_get_thermo_dt = lmp%get_thermo('dt')
END FUNCTION f_lammps_get_thermo_dt
FUNCTION f_lammps_get_thermo_vol () BIND (C)
FUNCTION f_lammps_get_thermo_vol() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_vol
REAL(c_double) :: f_lammps_get_thermo_vol
f_lammps_get_thermo_vol = lmp%get_thermo('vol')
END FUNCTION f_lammps_get_thermo_vol
FUNCTION f_lammps_get_thermo_lx () BIND (C)
FUNCTION f_lammps_get_thermo_lx() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_lx
REAL(c_double) :: f_lammps_get_thermo_lx
f_lammps_get_thermo_lx = lmp%get_thermo('lx')
END FUNCTION f_lammps_get_thermo_lx
FUNCTION f_lammps_get_thermo_ly () BIND (C)
FUNCTION f_lammps_get_thermo_ly() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_ly
REAL(c_double) :: f_lammps_get_thermo_ly
f_lammps_get_thermo_ly = lmp%get_thermo('ly')
END FUNCTION f_lammps_get_thermo_ly
FUNCTION f_lammps_get_thermo_lz () BIND (C)
FUNCTION f_lammps_get_thermo_lz() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_lz
REAL(c_double) :: f_lammps_get_thermo_lz
f_lammps_get_thermo_lz = lmp%get_thermo('lz')
END FUNCTION f_lammps_get_thermo_lz
FUNCTION f_lammps_get_thermo_xlo () BIND (C)
FUNCTION f_lammps_get_thermo_xlo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_xlo
REAL(c_double) :: f_lammps_get_thermo_xlo
f_lammps_get_thermo_xlo = lmp%get_thermo('xlo')
END FUNCTION f_lammps_get_thermo_xlo
FUNCTION f_lammps_get_thermo_xhi () BIND (C)
FUNCTION f_lammps_get_thermo_xhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_xhi
REAL(c_double) :: f_lammps_get_thermo_xhi
f_lammps_get_thermo_xhi = lmp%get_thermo('xhi')
END FUNCTION f_lammps_get_thermo_xhi
FUNCTION f_lammps_get_thermo_ylo () BIND (C)
FUNCTION f_lammps_get_thermo_ylo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_ylo
REAL(c_double) :: f_lammps_get_thermo_ylo
f_lammps_get_thermo_ylo = lmp%get_thermo('ylo')
END FUNCTION f_lammps_get_thermo_ylo
FUNCTION f_lammps_get_thermo_yhi () BIND (C)
FUNCTION f_lammps_get_thermo_yhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_yhi
REAL(c_double) :: f_lammps_get_thermo_yhi
f_lammps_get_thermo_yhi = lmp%get_thermo('yhi')
END FUNCTION f_lammps_get_thermo_yhi
FUNCTION f_lammps_get_thermo_zlo () BIND (C)
FUNCTION f_lammps_get_thermo_zlo() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_zlo
REAL(c_double) :: f_lammps_get_thermo_zlo
f_lammps_get_thermo_zlo = lmp%get_thermo('zlo')
END FUNCTION f_lammps_get_thermo_zlo
FUNCTION f_lammps_get_thermo_zhi () BIND (C)
FUNCTION f_lammps_get_thermo_zhi() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (c_double) :: f_lammps_get_thermo_zhi
REAL(c_double) :: f_lammps_get_thermo_zhi
f_lammps_get_thermo_zhi = lmp%get_thermo('zhi')
END FUNCTION f_lammps_get_thermo_zhi

73
unittest/fortran/test_fortran_properties.f90
View File

@ -1,52 +1,89 @@
FUNCTION f_lammps_version () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_version() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER (C_int) :: f_lammps_version
INTEGER(c_int) :: f_lammps_version
f_lammps_version = lmp%version()
END FUNCTION f_lammps_version
SUBROUTINE f_lammps_memory_usage (meminfo) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
SUBROUTINE f_lammps_memory_usage(meminfo) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL (C_double), DIMENSION(3), INTENT(OUT) :: meminfo
REAL(c_double), DIMENSION(3), INTENT(OUT) :: meminfo
CALL lmp%memory_usage(meminfo)
END SUBROUTINE f_lammps_memory_usage
FUNCTION f_lammps_get_mpi_comm () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
FUNCTION f_lammps_get_mpi_comm() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER (C_int) :: f_lammps_get_mpi_comm
INTEGER(c_int) :: f_lammps_get_mpi_comm
f_lammps_get_mpi_comm = lmp%get_mpi_comm()
END FUNCTION f_lammps_get_mpi_comm
FUNCTION f_lammps_extract_setting (Cstr) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int, C_char
FUNCTION f_lammps_extract_setting(Cstr) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER (C_int) :: f_lammps_extract_setting
CHARACTER (KIND=C_char, LEN=1), DIMENSION(*), INTENT(IN) :: Cstr
INTEGER(c_int) :: f_lammps_extract_setting
CHARACTER(KIND=c_char, LEN=1), DIMENSION(*), INTENT(IN) :: Cstr
INTEGER :: strlen, i
CHARACTER (LEN=:), ALLOCATABLE :: Fstr
CHARACTER(LEN=:), ALLOCATABLE :: Fstr
i = 1
DO WHILE (Cstr(i) /= ACHAR(0))
i = i + 1
END DO
strlen = i
allocate ( CHARACTER(LEN=strlen) :: Fstr)
FORALL (i=1:strlen)
ALLOCATE(CHARACTER(LEN=strlen) :: Fstr)
DO i = 1, strlen
Fstr(i:i) = Cstr(i)
END FORALL
END DO
f_lammps_extract_setting = lmp%extract_setting(Fstr)
deallocate (Fstr)
DEALLOCATE(Fstr)
END FUNCTION f_lammps_extract_setting
FUNCTION f_lammps_has_error() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_has_error
IF (lmp%has_error()) THEN
f_lammps_has_error = 1_c_int
ELSE
f_lammps_has_error = 0_c_int
END IF
END FUNCTION f_lammps_has_error
FUNCTION f_lammps_get_last_error_message(errmesg, errlen) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_ptr, C_F_POINTER
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_get_last_error_message
CHARACTER(KIND=c_char), DIMENSION(*) :: errmesg
INTEGER(c_int), VALUE, INTENT(IN) :: errlen
CHARACTER(LEN=:), ALLOCATABLE :: buffer
INTEGER :: status, i
! copy error message to buffer
ALLOCATE(CHARACTER(errlen) :: buffer)
CALL lmp%get_last_error_message(buffer, status)
f_lammps_get_last_error_message = status
! and copy to C style string
DO i=1, errlen
errmesg(i) = buffer(i:i)
IF (buffer(i:i) == ACHAR(0)) EXIT
END DO
DEALLOCATE(buffer)
END FUNCTION f_lammps_get_last_error_message

6
unittest/fortran/wrap_box.cpp
View File

@ -55,10 +55,10 @@ TEST_F(LAMMPS_commands, get_thermo)
EXPECT_DOUBLE_EQ(f_lammps_extract_box_zhi(), 2.0);
f_lammps_delete_everything();
f_lammps_reset_box_2x();
EXPECT_DOUBLE_EQ(f_lammps_extract_box_xlo(),-1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_xlo(), -1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_xhi(), 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_ylo(),-1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_ylo(), -1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_yhi(), 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_zlo(),-1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_zlo(), -1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_box_zhi(), 3.0);
};

120
unittest/fortran/wrap_extract_atom.cpp Normal file
View File

@ -0,0 +1,120 @@
// unit tests for extracting Atom class data from a LAMMPS instance through the
// Fortran wrapper
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include "gtest/gtest.h"
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_extract_atom();
double f_lammps_extract_atom_mass();
int f_lammps_extract_atom_tag_int(int);
int64_t f_lammps_extract_atom_tag_int64(int64_t);
int f_lammps_extract_atom_type(int);
int f_lammps_extract_atom_mask(int);
void f_lammps_extract_atom_x(int, double *);
void f_lammps_extract_atom_v(int, double *);
}
class LAMMPS_extract_atom : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_atom() = default;
~LAMMPS_extract_atom() override = default;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_atom, mass)
{
f_lammps_setup_extract_atom();
EXPECT_DOUBLE_EQ(f_lammps_extract_atom_mass(), 2.0);
};
TEST_F(LAMMPS_extract_atom, tag)
{
f_lammps_setup_extract_atom();
#if defined(LAMMPS_BIGBIG)
EXPECT_EQ(f_lammps_extract_atom_tag_int64(1l), 1l);
EXPECT_EQ(f_lammps_extract_atom_tag_int64(2l), 2l);
#else
EXPECT_EQ(f_lammps_extract_atom_tag_int(1), 1);
EXPECT_EQ(f_lammps_extract_atom_tag_int(2), 2);
#endif
};
TEST_F(LAMMPS_extract_atom, type)
{
f_lammps_setup_extract_atom();
EXPECT_EQ(f_lammps_extract_atom_type(1), 1);
EXPECT_EQ(f_lammps_extract_atom_type(2), 1);
};
TEST_F(LAMMPS_extract_atom, mask)
{
f_lammps_setup_extract_atom();
EXPECT_EQ(f_lammps_extract_atom_mask(1), 1);
EXPECT_EQ(f_lammps_extract_atom_mask(2), 1);
lammps_command(lmp, "group 1 id 1");
lammps_command(lmp, "group 2 id 2");
EXPECT_EQ(f_lammps_extract_atom_mask(1), 3);
EXPECT_EQ(f_lammps_extract_atom_mask(2), 5);
};
TEST_F(LAMMPS_extract_atom, x)
{
f_lammps_setup_extract_atom();
double x1[3];
double x2[3];
f_lammps_extract_atom_x(1, x1);
EXPECT_DOUBLE_EQ(x1[0], 1.0);
EXPECT_DOUBLE_EQ(x1[1], 1.0);
EXPECT_DOUBLE_EQ(x1[2], 1.5);
f_lammps_extract_atom_x(2, x2);
EXPECT_DOUBLE_EQ(x2[0], 0.2);
EXPECT_DOUBLE_EQ(x2[1], 0.1);
EXPECT_DOUBLE_EQ(x2[2], 0.1);
}
TEST_F(LAMMPS_extract_atom, v)
{
f_lammps_setup_extract_atom();
double v1[3];
double v2[3];
f_lammps_extract_atom_v(1, v1);
EXPECT_DOUBLE_EQ(v1[0], 0.0);
EXPECT_DOUBLE_EQ(v1[1], 0.0);
EXPECT_DOUBLE_EQ(v1[2], 0.0);
f_lammps_extract_atom_v(2, v2);
EXPECT_DOUBLE_EQ(v2[0], 0.0);
EXPECT_DOUBLE_EQ(v2[1], 0.0);
EXPECT_DOUBLE_EQ(v2[2], 0.0);
lammps_command(lmp, "group one id 1");
lammps_command(lmp, "velocity one set 1 2 3");
f_lammps_extract_atom_v(1, v1);
EXPECT_DOUBLE_EQ(v1[0], 1.0);
EXPECT_DOUBLE_EQ(v1[1], 2.0);
EXPECT_DOUBLE_EQ(v1[2], 3.0);
}

168
unittest/fortran/wrap_extract_compute.cpp Normal file
View File

@ -0,0 +1,168 @@
// unit tests for extracting compute data from a LAMMPS instance through the
// Fortran wrapper
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include "gtest/gtest.h"
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_extract_compute();
double f_lammps_extract_compute_peratom_vector(int);
double f_lammps_extract_compute_peratom_array(int, int);
double f_lammps_extract_compute_global_scalar();
double f_lammps_extract_compute_global_vector(int);
double f_lammps_extract_compute_global_array(int, int);
double f_lammps_extract_compute_local_vector(int);
double f_lammps_extract_compute_local_array(int, int);
}
class LAMMPS_extract_compute : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_compute() = default;
~LAMMPS_extract_compute() override = default;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_compute, peratom_vector)
{
f_lammps_setup_extract_compute();
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_vector(1), -0.599703102447981);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_vector(2), 391.817623795857);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_vector(3), 391.430665759871);
};
TEST_F(LAMMPS_extract_compute, peratom_array)
{
f_lammps_setup_extract_compute();
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(1, 1), 0.8837067009319107);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(2, 1), 0.3588584939803668);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(3, 1), 1.2799807127711049);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(4, 1), 0.20477632346642258);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(5, 1), 0.400429511840588);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(6, 1), 0.673995757699694);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(1, 2), -1070.0291234709418);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(2, 2), -1903.651817128683);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(3, 2), -1903.5121520875714);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(4, 2), -1427.867483013);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(5, 2), -1427.8560790941347);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_peratom_array(6, 2), -1903.5971655908565);
};
TEST_F(LAMMPS_extract_compute, global_scalar)
{
f_lammps_setup_extract_compute();
double *scalar;
scalar = (double *)lammps_extract_compute(lmp, "totalpe", LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR);
// EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_scalar(), 782.64858645328);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_scalar(), *scalar);
};
TEST_F(LAMMPS_extract_compute, global_vector)
{
f_lammps_setup_extract_compute();
double *vector;
vector = (double *)lammps_extract_compute(lmp, "COM", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_vector(1), vector[0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_vector(2), vector[1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_vector(3), vector[2]);
};
TEST_F(LAMMPS_extract_compute, global_array)
{
f_lammps_setup_extract_compute();
double **array;
array = (double **)lammps_extract_compute(lmp, "RDF", LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(1, 1), array[0][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(2, 1), array[0][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(1, 2), array[1][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(2, 2), array[1][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(1, 3), array[2][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_global_array(1, 4), array[3][0]);
};
TEST_F(LAMMPS_extract_compute, local_vector)
{
f_lammps_setup_extract_compute();
double *vector;
vector = (double *)lammps_extract_compute(lmp, "pairdist", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(1), vector[0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(2), vector[1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(3), vector[2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(4), vector[3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(5), vector[4]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(6), vector[5]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(7), vector[6]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(8), vector[7]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(9), vector[8]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_vector(10), vector[9]);
};
TEST_F(LAMMPS_extract_compute, local_array)
{
f_lammps_setup_extract_compute();
double **array;
array = (double **)lammps_extract_compute(lmp, "pairlocal", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 1), array[0][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 1), array[0][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 1), array[0][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 1), array[0][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 2), array[1][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 2), array[1][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 2), array[1][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 2), array[1][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 3), array[2][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 3), array[2][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 3), array[2][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 3), array[2][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 4), array[3][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 4), array[3][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 4), array[3][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 4), array[3][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 5), array[4][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 5), array[4][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 5), array[4][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 5), array[4][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 6), array[5][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 6), array[5][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 6), array[5][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 6), array[5][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 7), array[6][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 7), array[6][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 7), array[6][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 7), array[6][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 8), array[7][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 8), array[7][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 8), array[7][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 8), array[7][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 9), array[8][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 9), array[8][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 9), array[8][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 9), array[8][3]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(1, 10), array[9][0]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(2, 10), array[9][1]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(3, 10), array[9][2]);
EXPECT_DOUBLE_EQ(f_lammps_extract_compute_local_array(4, 10), array[9][3]);
};

107
unittest/fortran/wrap_extract_fix.cpp Normal file
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@ -0,0 +1,107 @@
// unit tests for extracting compute data from a LAMMPS instance through the
// Fortran wrapper
#include <cstdio>
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include "gtest/gtest.h"
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_extract_fix();
double f_lammps_extract_fix_global_scalar();
double f_lammps_extract_fix_global_vector(int);
double f_lammps_extract_fix_global_array(int, int);
double f_lammps_extract_fix_peratom_vector(int);
double f_lammps_extract_fix_peratom_array(int, int);
double f_lammps_extract_fix_local_vector(int);
double f_lammps_extract_fix_local_array(int, int);
}
class LAMMPS_extract_fix : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_fix() = default;
~LAMMPS_extract_fix() override = default;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_fix, global_scalar)
{
f_lammps_setup_extract_fix();
double *scalar =
(double *)lammps_extract_fix(lmp, "recenter", LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR, -1, -1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_scalar(), *scalar);
lammps_free(scalar);
};
TEST_F(LAMMPS_extract_fix, global_vector)
{
f_lammps_setup_extract_fix();
double *x =
(double *)lammps_extract_fix(lmp, "recenter", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, -1);
double *y =
(double *)lammps_extract_fix(lmp, "recenter", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, -1);
double *z =
(double *)lammps_extract_fix(lmp, "recenter", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, -1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(1), *x);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(2), *y);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(3), *z);
lammps_free(x);
lammps_free(y);
lammps_free(z);
};
TEST_F(LAMMPS_extract_fix, global_array)
{
f_lammps_setup_extract_fix();
double natoms = lammps_get_natoms(lmp);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(1, 1), natoms);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(1, 2), natoms);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(2, 1), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(2, 2), 1.0);
};
TEST_F(LAMMPS_extract_fix, peratom_vector)
{
f_lammps_setup_extract_fix();
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(3), 0.5);
};
TEST_F(LAMMPS_extract_fix, peratom_array)
{
f_lammps_setup_extract_fix();
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3, 1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1, 2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3, 3), 0.5);
};

124
unittest/fortran/wrap_extract_global.cpp
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@ -3,10 +3,10 @@
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include <cstdlib>
#include <cstdint>
#include "gtest/gtest.h"
@ -78,100 +78,100 @@ protected:
TEST_F(LAMMPS_extract_global, units)
{
f_lammps_setup_extract_global();
EXPECT_EQ(f_lammps_extract_global_units(), 1);
f_lammps_setup_extract_global();
EXPECT_EQ(f_lammps_extract_global_units(), 1);
};
TEST_F(LAMMPS_extract_global, ntimestep)
{
f_lammps_setup_extract_global();
f_lammps_setup_extract_global();
#ifdef LAMMPS_SMALLSMALL
EXPECT_EQ(f_lammps_extract_global_ntimestep(), 0);
EXPECT_EQ(f_lammps_extract_global_ntimestep(), 0);
#else
EXPECT_EQ(f_lammps_extract_global_ntimestep_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_ntimestep_big(), 0l);
#endif
};
TEST_F(LAMMPS_extract_global, dt)
{
f_lammps_setup_extract_global();
EXPECT_DOUBLE_EQ(f_lammps_extract_global_dt(), 0.005);
f_lammps_setup_extract_global();
EXPECT_DOUBLE_EQ(f_lammps_extract_global_dt(), 0.005);
};
TEST_F(LAMMPS_extract_global, boxprops)
{
f_lammps_setup_extract_global();
double boxlo[3], boxhi[3];
f_lammps_extract_global_boxlo(boxlo);
EXPECT_DOUBLE_EQ(boxlo[0], 0.0);
EXPECT_DOUBLE_EQ(boxlo[1], 0.0);
EXPECT_DOUBLE_EQ(boxlo[2], 0.0);
f_lammps_extract_global_boxhi(boxhi);
EXPECT_DOUBLE_EQ(boxhi[0], 2.0);
EXPECT_DOUBLE_EQ(boxhi[1], 3.0);
EXPECT_DOUBLE_EQ(boxhi[2], 4.0);
f_lammps_setup_extract_global();
double boxlo[3], boxhi[3];
f_lammps_extract_global_boxlo(boxlo);
EXPECT_DOUBLE_EQ(boxlo[0], 0.0);
EXPECT_DOUBLE_EQ(boxlo[1], 0.0);
EXPECT_DOUBLE_EQ(boxlo[2], 0.0);
f_lammps_extract_global_boxhi(boxhi);
EXPECT_DOUBLE_EQ(boxhi[0], 2.0);
EXPECT_DOUBLE_EQ(boxhi[1], 3.0);
EXPECT_DOUBLE_EQ(boxhi[2], 4.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxxlo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxxhi(), 2.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxylo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxyhi(), 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxzlo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxzhi(), 4.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxxlo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxxhi(), 2.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxylo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxyhi(), 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxzlo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boxzhi(), 4.0);
int periodicity[3];
f_lammps_extract_global_periodicity(periodicity);
EXPECT_EQ(periodicity[0], 1);
EXPECT_EQ(periodicity[1], 1);
EXPECT_EQ(periodicity[2], 1);
int periodicity[3];
f_lammps_extract_global_periodicity(periodicity);
EXPECT_EQ(periodicity[0], 1);
EXPECT_EQ(periodicity[1], 1);
EXPECT_EQ(periodicity[2], 1);
EXPECT_EQ(f_lammps_extract_global_triclinic(), 0);
EXPECT_EQ(f_lammps_extract_global_triclinic(), 0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_xy(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_yz(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_xz(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_xy(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_yz(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_xz(), 0.0);
};
TEST_F(LAMMPS_extract_global, atomprops)
{
f_lammps_setup_extract_global();
f_lammps_setup_extract_global();
#ifdef LAMMPS_SMALLSMALL
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
#else
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
#endif
EXPECT_EQ(f_lammps_extract_global_ntypes(), 1);
EXPECT_EQ(f_lammps_extract_global_nlocal(), 2);
EXPECT_EQ(f_lammps_extract_global_nghost(), 41);
EXPECT_EQ(f_lammps_extract_global_nmax(), 16384);
EXPECT_EQ(f_lammps_extract_global_ntypes(), 1);
EXPECT_EQ(f_lammps_extract_global_nlocal(), 2);
EXPECT_EQ(f_lammps_extract_global_nghost(), 41);
EXPECT_EQ(f_lammps_extract_global_nmax(), 16384);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boltz(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_hplanck(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_angstrom(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_boltz(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_hplanck(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_angstrom(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_femtosecond(), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_global_femtosecond(), 1.0);
};
TEST_F(LAMMPS_extract_global, fullprops)
{
if (! lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
// This is not currently the world's most convincing test....
f_lammps_setup_full_extract_global();
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
// This is not currently the world's most convincing test....
f_lammps_setup_full_extract_global();
#ifdef LAMMPS_SMALLSMALL
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
#else
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
#endif
}

283
unittest/fortran/wrap_extract_variable.cpp Normal file
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@ -0,0 +1,283 @@
// unit tests for extracting compute data from a LAMMPS instance through the
// Fortran wrapper
#include "lammps.h"
#include "library.h"
#include "platform.h"
#include <chrono>
#include <cmath>
#include <cstdint>
#include <cstdio>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include <thread>
#include "gtest/gtest.h"
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_c_args(int, char **);
void f_lammps_close();
void f_lammps_setup_extract_variable();
int f_lammps_extract_variable_index_1();
int f_lammps_extract_variable_index_2();
int f_lammps_extract_variable_loop();
char *f_lammps_extract_variable_loop_pad();
char *f_lammps_extract_variable_world();
char *f_lammps_extract_variable_universe();
int f_lammps_extract_variable_uloop();
char *f_lammps_extract_variable_string();
char *f_lammps_extract_variable_format();
char *f_lammps_extract_variable_format_pad();
char *f_lammps_extract_variable_getenv();
char *f_lammps_extract_variable_file();
double f_lammps_extract_variable_atomfile(int);
double f_lammps_extract_variable_python();
double f_lammps_extract_variable_timer();
double f_lammps_extract_variable_internal();
double f_lammps_extract_variable_equal();
double f_lammps_extract_variable_atom(int);
double f_lammps_extract_variable_vector(int);
void f_lammps_set_variable_string();
char *c_path_join(const char *, const char *);
}
char *c_path_join(const char *a, const char *b)
{
std::string A = a;
std::string B = b;
std::string C = LAMMPS_NS::platform::path_join(A, B);
size_t length = C.length() + 1;
char *retval = (char *)malloc(length * sizeof(char));
C.copy(retval, length);
retval[length - 1] = '\0';
return retval;
}
constexpr char input_dir[] = STRINGIFY(TEST_INPUT_FOLDER);
class LAMMPS_extract_variable : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_variable() = default;
~LAMMPS_extract_variable() override = default;
void SetUp() override
{
// clang-format off
const char *args[] =
{ "LAMMPS_Fortran_test", "-l", "none", "-echo", "screen", "-nocite",
"-var", "input_dir", input_dir, "-var", "zpos", "1.5", "-var", "x", "2" };
// clang-format on
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(const char *);
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_c_args(argc, argv);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_variable, index)
{
f_lammps_setup_extract_variable();
EXPECT_EQ(f_lammps_extract_variable_index_1(), 1);
EXPECT_EQ(f_lammps_extract_variable_index_2(), 0);
lammps_command(lmp, "next idx");
EXPECT_EQ(f_lammps_extract_variable_index_1(), 0);
EXPECT_EQ(f_lammps_extract_variable_index_2(), 1);
};
TEST_F(LAMMPS_extract_variable, loop)
{
f_lammps_setup_extract_variable();
int i;
for (i = 1; i <= 10; i++) {
EXPECT_EQ(f_lammps_extract_variable_loop(), i);
lammps_command(lmp, "next lp");
}
};
TEST_F(LAMMPS_extract_variable, loop_pad)
{
f_lammps_setup_extract_variable();
int i;
char str[10];
char *fstr;
for (i = 1; i <= 10; i++) {
std::sprintf(str, "%02d", i);
fstr = f_lammps_extract_variable_loop_pad();
EXPECT_STREQ(fstr, str);
std::free(fstr);
lammps_command(lmp, "next lp_pad");
}
};
TEST_F(LAMMPS_extract_variable, world)
{
f_lammps_setup_extract_variable();
char *fstr = f_lammps_extract_variable_world();
EXPECT_STREQ(fstr, "group1");
std::free(fstr);
};
TEST_F(LAMMPS_extract_variable, universe)
{
f_lammps_setup_extract_variable();
char *fstr = f_lammps_extract_variable_universe();
EXPECT_STREQ(fstr, "universe1");
std::free(fstr);
};
TEST_F(LAMMPS_extract_variable, uloop)
{
f_lammps_setup_extract_variable();
EXPECT_EQ(f_lammps_extract_variable_uloop(), 1);
};
TEST_F(LAMMPS_extract_variable, string)
{
f_lammps_setup_extract_variable();
char *fstr = f_lammps_extract_variable_string();
EXPECT_STREQ(fstr, "this is a string");
std::free(fstr);
f_lammps_set_variable_string();
fstr = f_lammps_extract_variable_string();
EXPECT_STREQ(fstr, "this is the new string");
std::free(fstr);
};
TEST_F(LAMMPS_extract_variable, format)
{
f_lammps_setup_extract_variable();
int i;
char str[16];
char *fstr;
for (i = 1; i <= 10; i++) {
std::sprintf(str, "%.6G", std::exp(i));
fstr = f_lammps_extract_variable_format();
EXPECT_STREQ(fstr, str);
std::free(fstr);
lammps_command(lmp, "next lp");
}
};
TEST_F(LAMMPS_extract_variable, format_pad)
{
f_lammps_setup_extract_variable();
int i;
char str[16];
char *fstr;
for (i = 1; i <= 10; i++) {
std::sprintf(str, "%08.6G", std::exp(i));
fstr = f_lammps_extract_variable_format_pad();
EXPECT_STREQ(fstr, str);
std::free(fstr);
lammps_command(lmp, "next lp");
}
};
TEST_F(LAMMPS_extract_variable, getenv)
{
LAMMPS_NS::platform::putenv("FORTRAN_USER=myuser");
f_lammps_setup_extract_variable();
char *env = std::getenv("FORTRAN_USER");
char *fenv = f_lammps_extract_variable_getenv();
EXPECT_STREQ(fenv, env);
std::free(fenv);
};
TEST_F(LAMMPS_extract_variable, file)
{
f_lammps_setup_extract_variable();
int i;
const char *str[9] = {"hello", "god_dag", "hola", "bonjour", "guten_Tag",
"konnichiwa", "shalom", "salve", "goedendag"};
char *fstr;
for (i = 0; i < 9; i++) {
fstr = f_lammps_extract_variable_file();
EXPECT_STREQ(fstr, str[i]);
std::free(fstr);
lammps_command(lmp, "next greeting");
}
};
TEST_F(LAMMPS_extract_variable, atomfile)
{
f_lammps_setup_extract_variable();
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(1), 5.2);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(2), 1.6);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(3), -1.4);
lammps_command(lmp, "next atfile");
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(1), -1.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(2), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(3), 2.5);
};
TEST_F(LAMMPS_extract_variable, python)
{
if (lammps_config_has_package("PYTHON")) {
f_lammps_setup_extract_variable();
for (int i = 1; i <= 10; i++) {
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_python(), static_cast<double>(i * i));
lammps_command(lmp, "next lp");
}
}
};
TEST_F(LAMMPS_extract_variable, timer)
{
f_lammps_setup_extract_variable();
double initial_t, final_t;
initial_t = f_lammps_extract_variable_timer();
std::this_thread::sleep_for(std::chrono::milliseconds(100));
lammps_command(lmp, "variable time timer"); // update the time
final_t = f_lammps_extract_variable_timer();
EXPECT_GT(final_t, initial_t + 0.1);
};
TEST_F(LAMMPS_extract_variable, internal)
{
f_lammps_setup_extract_variable();
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_internal(), 4.0);
};
TEST_F(LAMMPS_extract_variable, equal)
{
f_lammps_setup_extract_variable();
int i;
for (i = 1; i <= 10; i++) {
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_equal(), std::exp(static_cast<double>(i)));
lammps_command(lmp, "next lp");
}
};
TEST_F(LAMMPS_extract_variable, atom)
{
f_lammps_setup_extract_variable();
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atom(1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atom(2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atom(3), 0.5);
};
TEST_F(LAMMPS_extract_variable, vector)
{
f_lammps_setup_extract_variable();
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_vector(1), (1 + 0.2 + 0.5) / 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_vector(2), (1 + 0.1 + 0.5) / 3.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_variable_vector(3), (1.5 + 0.1 + 0.5) / 3.0);
};

202
unittest/fortran/wrap_gather_scatter.cpp Normal file
View File

@ -0,0 +1,202 @@
// unit tests for gathering and scattering data from a LAMMPS instance through
// the Fortran wrapper
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <cstdlib>
#include <mpi.h>
#include <string>
#include "gtest/gtest.h"
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_gather_scatter();
int f_lammps_gather_atoms_mask(int);
double f_lammps_gather_atoms_position(int);
int f_lammps_gather_atoms_concat_mask(int);
double f_lammps_gather_atoms_concat_position(int, int);
int f_lammps_gather_atoms_subset_mask(int);
double f_lammps_gather_atoms_subset_position(int, int);
void f_lammps_scatter_atoms_masks();
void f_lammps_scatter_atoms_positions();
}
class LAMMPS_gather_scatter : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_gather_scatter() = default;
~LAMMPS_gather_scatter() override = default;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_masks)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 1);
EXPECT_EQ(f_lammps_gather_atoms_mask(2), 1);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 1);
lammps_command(lmp, "group special id 1");
lammps_command(lmp, "group other id 2");
lammps_command(lmp, "group spiffy id 3");
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 3);
EXPECT_EQ(f_lammps_gather_atoms_mask(2), 5);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 9);
lammps_command(lmp, "group other id 1");
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 7);
EXPECT_EQ(f_lammps_gather_atoms_mask(2), 5);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 9);
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_positions)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(2), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(3), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(4), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(5), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(6), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(7), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(8), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_position(9), 0.5);
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_concat_masks)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(1), 1);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(2), 1);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(3), 1);
lammps_command(lmp, "group special id 1");
lammps_command(lmp, "group other id 2");
lammps_command(lmp, "group spiffy id 3");
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(1), 3);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(2), 5);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(3), 9);
lammps_command(lmp, "group other id 1");
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(1), 7);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(2), 5);
EXPECT_EQ(f_lammps_gather_atoms_concat_mask(3), 9);
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_concat_positions)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 3), 0.5);
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_subset_masks)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(2), 1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(3), 1);
lammps_command(lmp, "group special id 1");
lammps_command(lmp, "group other id 2");
lammps_command(lmp, "group spiffy id 3");
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(2), 5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(3), 9);
lammps_command(lmp, "group other id 3");
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(2), 5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_mask(3), 13);
};
TEST_F(LAMMPS_gather_scatter, gather_atoms_subset_positions)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(1, 2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(2, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(3, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(1, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(2, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_subset_position(3, 3), 0.5);
};
TEST_F(LAMMPS_gather_scatter, scatter_atoms_masks)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
lammps_command(lmp, "group special id 1");
lammps_command(lmp, "group other id 2");
lammps_command(lmp, "group spiffy id 3");
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(1), 3);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(2), 5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(3), 9);
f_lammps_scatter_atoms_masks();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(1), 9);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(2), 5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_mask(3), 3);
};
TEST_F(LAMMPS_gather_scatter, scatter_atoms_positions)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 3), 0.5);
f_lammps_scatter_atoms_positions();
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 3), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 3), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 3), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(1, 1), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(2, 1), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_gather_atoms_concat_position(3, 1), 0.5);
};
TEST_F(LAMMPS_gather_scatter, scatter_atoms_subset_mask)
{
if (lammps_extract_setting(nullptr, "tagint") == 8) GTEST_SKIP();
f_lammps_setup_gather_scatter();
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 1);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 1);
lammps_command(lmp, "group special id 1");
lammps_command(lmp, "group other id 2");
lammps_command(lmp, "group spiffy id 3");
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 3);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 9);
f_lammps_scatter_atoms_masks();
EXPECT_EQ(f_lammps_gather_atoms_mask(1), 9);
EXPECT_EQ(f_lammps_gather_atoms_mask(3), 3);
};

70
unittest/fortran/wrap_properties.cpp
View File

@ -2,9 +2,10 @@
#include "lammps.h"
#include "library.h"
#include <mpi.h>
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
// prototypes for fortran reverse wrapper functions
@ -12,24 +13,30 @@ extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
int f_lammps_version();
void f_lammps_memory_usage(double*);
void f_lammps_memory_usage(double *);
int f_lammps_get_mpi_comm();
int f_lammps_extract_setting(const char*);
int f_lammps_extract_setting(const char *);
int f_lammps_has_error();
int f_lammps_get_last_error_message(char *, int);
}
namespace LAMMPS_NS {
using ::testing::ContainsRegex;
class LAMMPS_properties : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_properties() = default;
~LAMMPS_properties() override = default;
LAMMPS *lmp;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
lmp = (LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
@ -47,10 +54,10 @@ TEST_F(LAMMPS_properties, version)
TEST_F(LAMMPS_properties, memory_usage)
{
// copied from c-library, with a two-character modification
double meminfo[3];
f_lammps_memory_usage(meminfo);
EXPECT_GT(meminfo[0], 0.0);
// copied from c-library, with a two-character modification
double meminfo[3];
f_lammps_memory_usage(meminfo);
EXPECT_GT(meminfo[0], 0.0);
#if defined(__linux__) || defined(_WIN32)
EXPECT_GE(meminfo[1], 0.0);
#endif
@ -61,11 +68,11 @@ TEST_F(LAMMPS_properties, memory_usage)
TEST_F(LAMMPS_properties, get_mpi_comm)
{
int f_comm = f_lammps_get_mpi_comm();
if ( lammps_config_has_mpi_support() )
EXPECT_GE(f_comm, 0);
else
EXPECT_EQ(f_comm, -1);
int f_comm = f_lammps_get_mpi_comm();
if (lammps_config_has_mpi_support())
EXPECT_GE(f_comm, 0);
else
EXPECT_EQ(f_comm, -1);
};
TEST_F(LAMMPS_properties, extract_setting)
@ -104,5 +111,34 @@ TEST_F(LAMMPS_properties, extract_setting)
EXPECT_EQ(f_lammps_extract_setting("mu_flag"), 0);
EXPECT_EQ(f_lammps_extract_setting("rmass_flag"), 0);
EXPECT_EQ(f_lammps_extract_setting("UNKNOWN"), -1);
};
TEST_F(LAMMPS_properties, has_error)
{
// need errors to throw exceptions to be able to intercept them.
if (!lammps_config_has_exceptions()) GTEST_SKIP();
EXPECT_EQ(f_lammps_has_error(), lammps_has_error(lmp));
EXPECT_EQ(f_lammps_has_error(), 0);
// trigger an error, but hide output
::testing::internal::CaptureStdout();
lammps_command(lmp, "this_is_not_a_known_command");
::testing::internal::GetCapturedStdout();
EXPECT_EQ(f_lammps_has_error(), lammps_has_error(lmp));
EXPECT_EQ(f_lammps_has_error(), 1);
// retrieve error message
char errmsg[1024];
int err = f_lammps_get_last_error_message(errmsg, 1023);
EXPECT_EQ(err, 1);
EXPECT_THAT(errmsg, ContainsRegex(".*ERROR: Unknown command: this_is_not_a_known_command.*"));
// retrieving the error message clear the error status
EXPECT_EQ(f_lammps_has_error(), 0);
err = f_lammps_get_last_error_message(errmsg, 1023);
EXPECT_EQ(err, 0);
EXPECT_THAT(errmsg, ContainsRegex(" "));
};
} // namespace LAMMPS_NS

2
unittest/tools/test_lammps_shell.py
View File

@ -138,7 +138,7 @@ class LammpsShell(unittest.TestCase):
for line in lines:
if line.startswith('LAMMPS Shell>'): break
idx += 1
self.assertEqual(lines[idx+4],"dimension 2")
self.assertEqual(lines[idx+6],"units real")
self.assertEqual(lines[idx+8],"dimension 2")

4
unittest/utils/testshared.c
View File

@ -16,5 +16,5 @@ double some_double_function(double arg1, int arg2)
return sum;
}