Minor updates in documentation and setup tool, merge before upgrade to oxDNA2

lmp_linux_double

The precision (single, mixed, double) refers to the GPU and USER-CUDA

pacakge precision.  See the README files in the lib/gpu and lib/cuda

package precision.  See the README files in the lib/gpu and lib/cuda

directories for instructions on how to build the packages with

different precisions.  The GPU and USER-CUDA sub-sections of the

doc/Section_accelerate.html file also describes this process.

/html

/spelling

/LAMMPS.epub

/LAMMPS.mobi

/Manual.pdf

SOURCES=$(wildcard src/*.txt)

OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

.PHONY: help clean-all clean epub html pdf old venv

.PHONY: help clean-all clean epub html pdf old venv spelling

# ------------------------------------------

clean:

	rm -rf $(RSTDIR) html

	rm -rf spelling

clean-spelling:

	rm -rf spelling

html: $(OBJECTS)

	@(\

	@rm -rf html/USER/*/*.[sg]*

	@echo "Build finished. The HTML pages are in doc/html."

spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt

	@(\

		. $(VENV)/bin/activate ;\

		pip install sphinxcontrib-spelling ;\

		cp -r src/* $(RSTDIR)/ ;\

        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\

		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\

		deactivate ;\

	)

	@echo "Spell check finished."

epub: $(OBJECTS)

	@mkdir -p epub

	@rm -f LAMMPS.epub

  entirely rigid (e.g. water)

the angletype option enables an additional check when SHAKE constraints

  are computed: if a cluster is of size 3 and both bonds in

  the cluster are of a bondtype specified by the 2nd paramter of

  the cluster are of a bondtype specified by the 2nd parameter of

  angletype, then the cluster is SHAKEn with an additional angle

  constraint that makes it rigid, using the equilibrium angle appropriate

  to the specified angletype

  since they will not be SHAKEn but neither will the angle force by computed

for style region, a coeff of INF means + or - infinity (all the way 

  to the boundary)

an atom can be assigned to multiple constraints, the contraints will be

an atom can be assigned to multiple constraints, the constraints will be

  applied in the reverse order they are assigned to that atom

  (e.g. each timestep, the last fix assigned to an atom will be applied 

  to it first, then the next-to-last applied second, etc)

         remainder

               no other parameters required

used with "create temp" commmand to initialize velocities of atoms

used with "create temp" command to initialize velocities of atoms

by default, the "create temp" command initializes the velocities of all atoms,

  this command limits the initialization to a group of atoms

this command is only in force for the next "create temp" command, any

  applied when atoms move except for the following

fixes associated with temperature control are not allowed

  (rescale, hoover/drag, langevin)

the minimizer does not invoke the "fix style shake" contraints on

the minimizer does not invoke the "fix style shake" constraints on

  bond lengths

the minimizer does not invoke pressure control or volume control settings

for good convergence, should specify use of smooth nonbond force fields 

  can be used that are supported by native machine libraries

this command is optional - if not used, a default

  mesh size will be chosen to satisfy accuracy criterion - if used, the

  specifed mesh size will override the default

  specified mesh size will override the default

</PRE>

<HR>

<H3>

when the minimizer is invoked this command means create a restart file

  at the end of the minimization with the filename filename.timestep.min

a restart file stores atom and force-field information in binary form

allows program to restart from where it left off (see "read restart" commmand)

allows program to restart from where it left off (see "read restart" command)

Default = 0

</PRE>

<P>

(6) flow</P>

<P>

2-d flow of Lennard-Jones atoms in a channel using various contraint 

2-d flow of Lennard-Jones atoms in a channel using various constraint

options.</P>

<P>

(7) polymer</P>

(compile and link with print.c) which can be used to generate random 

initial polymer configurations for bead-spring models like those used 

in examples/polymer. It uses an input polymer definition file (see 

examples/polymer for two sample def files) that specfies how many 

examples/polymer for two sample def files) that specifies how many

chains of what length, a random number seed, etc.</P>

</BODY>

</HTML>