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Example with GnuPlot
Seeexamples/COUPLE/simple for C, C++, Fortran
Seepython/examplesfor Python, Pizza.py for GnuPlot wrapper
% python plot.py in.lammps Nfreq Nsteps compute-ID
from gnu import gnu
from lammps import lammps
lmp = lammps()
lmp.file(infile)
lmp.command("thermo %d" % Nfreq)
lmp.command("run 0 pre yes post no")
value = lmp.extract
compute(computeID,0,0)
ntimestep = 0
xaxis = [ntimestep]
yaxis = [value]
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Example with GnuPlot (continued)
if me == 0:
gn = gnu()
gn.plot(xaxis,yaxis)
gn.xrange(0,nsteps)
gn.title(computeID,"Timestep","Temperature")
while ntimestep < Nsteps:
lmp.command("run %d pre no post no" % Nfreq)
ntimestep += nfreq
value = lmp.extract
compute(computeID,0,0)
xaxis.append(ntimestep)
yaxis.append(value)
if me == 0: gn.plot(xaxis,yaxis)
lmp.command("run 0 pre no post yes")
C# PDF Text Extract Library: extract text content from PDF file in
Able to extract and get all and partial text content from PDF file. How to C#: Extract Text Content from PDF File. Add necessary references:
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Extract and get partial and all text content from PDF file. Extract highlighted text out of PDF document. Extract Text Content from PDF File in VB.NET.
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What it produces, in real time
This includes GUI slider & dump output to Pizza.py GL tool
(or AtomEye or Pymol or VMD) - see python/examples scripts
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Microsoft Office Word, Excel and PowerPoint data to PDF form. Merge PDF with byte array, fields. Merge PDF without size limitation. Append one PDF file to the end
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Extending the LAMMPS library interface
Again, seelibrary.cpp andlibrary.h
Accessor functionsalreadyexistfor...
system variables (box, timestep, etc)
per-atom pointers (x, v, etc)
compute and x output
variable evaluation
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Extending the LAMMPS library interface
Again, seelibrary.cpp andlibrary.h
Accessor functionsalreadyexistfor...
system variables (box, timestep, etc)
per-atom pointers (x, v, etc)
compute and x output
variable evaluation
Accessor functions in library.cpp or atom.h can beaugmented
one-line addition
access a new system variable
access a new per-atom property
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By using RsterEdge XDoc PDF SDK for .NET, VB.NET users are able to extract image from PDF page or file and specified region on PDF page, then get image
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Extending the LAMMPS library interface
Again, seelibrary.cpp andlibrary.h
Accessor functionsalreadyexistfor...
system variables (box, timestep, etc)
per-atom pointers (x, v, etc)
compute and x output
variable evaluation
Accessor functions in library.cpp or atom.h can beaugmented
one-line addition
access a new system variable
access a new per-atom property
New functionsinlibrary.cppcan...
access any public data within LAMMPS
invoke any public methods of any classes
New functions are limited only by yourimagination!
How a timestep works - part 1
Most important class to understand: Verlet) src/verlet.cpp
How a timestep works - part 1
Most important class to understand: Verlet) src/verlet.cpp
Look at therun() method (in 3 parts)
See doc/Developer.pdf for more details
loop over N N timesteps:
ev
set()
fix->initial
integrate()
fix->post
integrate()
...
How a timestep works - part 2
loop over N timesteps:
...
nflag = neighbor->decide()
if nflag:
fix->pre
exchange()
domain->pbc()
domain->reset
box()
comm->setup()
neighbor->setup
bins()
comm->exchange()
comm->borders()
fix->pre
neighbor()
neighbor->build()
else
comm->forward
comm()
...
How a timestep works - part 3
loop over N timesteps:
...
force
clear()
fix->pre
force()
pair->compute()
bond->compute()
angle->compute()
dihedral->compute()
improper->compute()
kspace->compute()
comm->reverse
comm()
fix->post
force()
fix->final
integrate()
fix->end
of
step()
if any output on this step: output->write()
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