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<a name="top"></a>MCCCS Towhee (code manual)</font></b> </font>
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<td width="700" valign="top"> <b>Overview</b>
<ul>
This section explains the general structure of the Towhee program and also includes instructions on compiling Towhee. This page is only maintained
for the current version of the Towhee code. It was last updated for version 6.2.14.
</ul>
<b>Compiling</b>
<ul>
Towhee versions 3.9.8 or later have a sophisticated configure and Makefile setup that should allow automatic setting of the Makefile parameters on
most platforms. This requires the use of two fairly standard freely available programs.
<dt><a href="http://ftp.gnu.org/gnu/autoconf/">autoconf</a> Version 2.59 or later and</dt>
<dt><a href="http://www.gnu.org/software/automake/">automake</a> Version 1.7.4 or later</dt>
<p></p>
<font color="red">Compiling on a Unix/Linux Operating System using compilers similar to GNU</font>
<dt>In the top level directory issue the command</dt>
<dt><b>./configure</b></dt>
This should automatically set up Makefiles in the Source directory which will create an optimal build for your machine. Then go into the Source
directory
<dt><b>cd Source</b></dt>
and type
<dt><b>make towhee</b></dt>
Please note that the majority of compilations on Linux machines will require the
<dt><b>./configure --enable-fix-GNU</b></dt>
option to be turned on. Please see the Configure Options Section below for more information.
<p></p>
<font color="red">Compiling on an Apple OS-X Operating System</font>
<dt>Useful instructions and software for high performance computing on OS-X is available at
<a href="http://hpc.sourceforge.net/">http://hpc.sourceforge.net/</a>.
</dt>
<dt>Compiling Towhee on OS-X is very similar to compiling on a Unix/Linux operating system. Users on older versions
of OS-X may experience something similar to the following error message when they compile.
<ul>
<dt>ld: Undefined symbols:</dt>
<dt>restFP</dt>
<dt>saveFP</dt>
<dt>make: *** [towhee] Error 1</dt>
</ul>
</dt>
If this happens then you need to configure including the following option
<dt><b>./configure LDFLAGS=-lcc_dynamic</b></dt>
and recompile.
<p></p>
<font color="red">Compiling on a Windows Operating System using Cygwin</font>
<dt>Towhee is designed for compilation in a Unix style environment. In order to compile on a Windows machine we suggest the freely available
<a href="http://www.cygwin.com/">Cygwin</a> software. Once you have installed the Cygwin environment, and the appropriate additional software
(Fortran compiler, C compiler, autoconf and automake) you then follow the normal Towhee compilation procedure with one important exception. Cygwin
appends a '.exe' to any executable so the commands for compilation include an extra '.exe' compared with the Unix/Linux environment.
</dt>
<dt><b>./configure</b></dt>
<dt><b>cd Source</b></dt>
<dt><b>make towhee.exe</b></dt>
<p></p>
<font color="red">Compiling on a Windows Operating System using Intel's Visual Fortran and Microsoft's Visual C++. </font>
<dt> In addition to the standard towhee code, the following standard unix functionality is provided:
<ul>
<li> dirent.h : <a href="http://www.softagalleria.net/dirent.php">dirent</a> API for MSVC++ (located in towhee-x.x.xx\vs_towhee\dirent) </li>
<li> unistd.h : a subset of the complete Unix file is used (located in towhee-x.x.xx\vs_towhee\dirent)</li>
<li> getopt: <a href="http://argtable.sourceforge.net">atgtable</a> is an ANSI C library for parsing GNU style command line
options (located in towhee-x.x.xx\vs_towhee\argtable2-12)</li>
</ul>
</dt>
<dt>Microsoft Visual Studio 2008 and Intel Visual Fortran (11.1.xxx) should be installed. Fortran libraries path should be added
in the CV++ directories (Tools/Options | Projects and Solutions | VC++ Directories). Open the towhee solution
(towhee-x.x.xx\vs_towhee\towhee\towhee.sln), select the desired configuration and press build. The produced executables will
be placed under towhee-x.x.xx\vs_towhee\towhee\Release directory for the release configuration. Please note that the mpi
version is not currently supported.</dt>
<p></p>
<font color="red">Configure options in Towhee</font>
<ul>
<li><b>./configure --enable-safe-compare</b>
<dt>Using this flag turns on some slightly more expensive comparison routines that serve to make the results for the Examples exactly match between
different machines. It also sets bounds checking and turns on compiler warning messages. This option is used to create the answer_current
and par_answer_current files in the Examples directory.
</dt>
</li>
<li><b>./configure --enable-mpi</b>
<dt>This option builds an MPI version of Towhee. Note that for some machines it is actually easier to get the machine to compile using the MPI
options and you can still run single processor jobs with this version. Consult the
<a href="../towhee_parallel.html">towhee_parallel</a> manual for more information about this option.
</dt>
</li>
<li><b>./configure --enable-fix-GNU</b>
<dt>This option turns on the -fno-second-underscore flag on the fortran compile line in order to remove double underscores trailing a routine when there
is already an underscore in the routine name. If you are seeing errors that involve double underscores, such as
<ul>undefined reference to '_twh_moltyp__'</ul>
and you are using the GNU compilers, then this option might solve your problems.
</dt>
</li>
<li><b>./configure --enable-internal</b>
<dt>Some compilers do not include the error function intrinsics. Towhee includes some internal versions of the error function routines for use
when the intrinsics are lacking and this option forces Towhee to use the internally provided functions instead of the intrinsic versions.
</dt>
</li>
<li><b>./configure FFLAGS='-fbounds-check'</b>
<dt>where the items between the single quotes are the flags used for the Fortran compilation.</dt>
</li>
<li><b>./configure F77='pgf77' CC='pgcc'</b>
<dt>Sets the Fortran and C compilers to user specified values. This example shows the command needed to set the compilers to PGI pgf77 and pgcc</dt>
</li>
<li><b>./configure ADDLIB='-L/usr/whoever/lib/'</b>
<dt>Adds user specified libraries into the link command.</dt>
</li>
<li><b>./configure --enable-tramonto</b>
<dt>Links the Tramonto classical density functional code into Towhee for use as a really fancy implicit solvent. This option requires access to
the Tramonto code compiled as a library. See the <a href="http://software.sandia.gov/DFTfluids/">Tramonto</a> web site for more information.
</dt>
</li>
<li><b>./configure --enable-lcao</b>
<dt>Links the Quest quantum density functional code into Towhee for use as a really expensive force field. This option requires access to the
Quest code compiled as a library. See the <a href="http://dft.sandia.gov/Quest/">Quest</a> web site for more information.
</dt>
</li>
<li><b>./configure --disable-command-line-args</b>
<dt>Removes the ability of the code to read command line arguments. This also defaults to a parallel style of "jobfarm" when combined with
an --enable-mpi configure option. This option exists for users whose machines are unable to properly handle command line arguments, especially
for certain parallel machines.
</dt>
</li>
<li><b>./configure FFLAGS=''</b>
<dt>This turns off all of the Fortran compiler flags. This is useful when compiling the forcefield utility as some of the subroutines for assigning
force field parameters are so large that optmization can cause some machines to run out of memory.
</dt>
</li>
</ul>
<p></p>
<font color="red">Compiling the lcao version on the srnsquall machine</font>
<ul>
<dt>The srnsquall machine at Sandia was the main development platform for the combination of Towhee with the Quest quantum DFT code. The procedure
for compiling the combined version has been simplified.
<li><b>./configure --enable-internal --enable-mpi --enable-lcao --enable-link-srnsquall ADDLIB=-L/questpath</b>
<dt>where <b>questpath</b> is replaced with the directory path that contains the liblcao.a library. You also need
to edit the Source/Makefile produced by this configure to remove two spurious <b>'</b> symbols that appears in the link line.
</dt>
</li>
</dt>
</ul>
<p></p>
<font color="red">Compiling the lcao version on the Spirit machine</font>
<ul>
<dt>These are the directions for compiling the Towhee-LCAO version on the Sandia computer Spirit.
<li><b>./configure --enable-mpi --enable-lcao --enable-link-spirit ADDLIB=-L/questpath</b>
<dt>where <b>questpath</b> is replaced with the directory path that contains the liblcao.a library. An lcao library is in the publicly
readable /home/marmart/Lib directory on that machine so using that as the <b>questpath</b> should work properly.
</dt>
</li>
</dt>
</ul>
<font color="red">Compiling the forcefield utlitity</font>
<ul>
Please note that the vast majority of users only need to compile the towhee portion of the code and do not need the forcefield utility as that is only
required if you wish to generate the towhee_ff files. As the towhee_ff files come packaged with the download, and the forcefield utility contains
routines that are large enough to give some compilers trouble, you should not attempt to compile that package unless you know why you want it.
<dt><b>cd Source</b></dt>
<dt><b>make forcefield</b></dt>
</ul>
</ul>
<b>The .h files</b>
<ul>
<li><b><a name="preproc">preproc.h</a></b>
<dt>The preproc.h file is the only program file that a casual user will ever need to modify. This file contains parameters which control the
dimensions of many of the most important arrays in Towhee. Depending on your preproc.h settings, and the simulation you are trying to perform,
the code may produce an error message informing you that some variable exceeds some other variable. If that is the case then you will need to
modify the appropriate variable in preproc.h in order to accommodate your system. You also might need to decrease some of the variables in
preproc.h if your machine does not have enough memory for the arrays. Finally, some of the variables in preproc.h control certain settings that
almost never change, but may be useful for debugging purposes.
</dt>
</li>
<ul>
<li><b><a name="MAXBOX">MAXBOX</a></b> the maximum number of simulation boxes in the system.
Minimum value of MAXBOX is 1. No Maximum value for MAXBOX, but if it is set to more than 10 boxes then the pdb output will no longer function
properly.
</li>
<li><b><a name="NUMAX">NUMAX</a></b> the maximum number of atoms in any molecule. Minimum value is 1. No maximum value.</li>
<li><b><a name="NTMAX">NTMAX</a></b> the maximum number of types of molecules in the simulation. Minimum value is 1. No maximum value.</li>
<li><b><a name="MAXKMAX">MAXKMAX</a></b> the maximum value for <b>kmax</b> in the Ewald sum. Minimum value is 1. No maximum value.</li>
<li><b><a name="VECTORMAX">VECTORMAX</a></b> the maximum number of reciprocal space vectors in the Ewald sum.
Starting with version 3.17.0 this variable is set based upon the value of <b>MAXKMAX</b>.
</li>
<li><b><a name="MAXBLOCK">MAXBLOCK</a></b> the maximum number of blocks for the block averaging. Minimum value is 1. No maximum value.</li>
<li><b><a name="FLDMAX">FLDMAX</a></b> the maximum number of external fields in the system. Minimum value is 1. No maximum value.</li>
<li><b><a name="NNTYPE">NNTYPE</a></b> the maximum number of different types of atoms allowed in the simulation.</li>
<li><b><a name="CROSSTYPEMAX">CROSSTYPEMAX</a></b> the maximum number of cross types, currently set to depend upon NNTYPE.</li>
<li><b><a name="MAXTABTYPE">MAXTABTYPE</a></b> the maximum number of types of atoms for tabular potentials.
Minimum value is 1. Maximum value is NNTYPE.
</li>
<li><b><a name="MAXTABLE">MAXTABLE</a></b> the maximum number of entries to describe a tabular potential.
Minimum value is 1. Maximum value is NNTYPE.
</li>
<li><b><a name="TVIBMAX">TVIBMAX</a></b> the maximum number of different types of vibrations in the simulation.</li>
<li><b><a name="TBENMAX">TBENMAX</a></b> the maximum number of different types of bending angles in the simulation.</li>
<li><b><a name="TTORMAX">TTORMAX</a></b> the maximum number of different types of regular torsions in the simulation.</li>
<li><b><a name="TIMPMAX">TIMPMAX</a></b> the maximum number of different types of improper torsions in the simulation.</li>
<li><b><a name="TAAMAX">TAAMAX</a></b> the maximum number of different types of angle-angle terms in the simulation.</li>
<li><b><a name="TOFMAX">TOFMAX</a></b> the maximum number of different types of special one-five terms in the simulation.</li>
<li><b><a name="THBONDMAX">THBONDMAX</a></b> the maximum number of different types of special hydrogen bond force field terms in the simulation.</li>
<li><b><a name="TBIMAX">TBIMAX</a></b> the maximum number of different types of bond increment terms in the simulation.</li>
<li><b><a name="NNBOND">NNBOND</a></b> the maximum number of bonds from any atom.
Minimum value is 1. No maximum value, and currently set to a default of 6.
</li>
<li><b><a name="MMBOND">MMBOND</a></b> the maximum number of bonds from any atom for use in computing the maximum number of all of the intramolecular
terms that are not just the number of vibrations. It is completely safe to set this to the same value as <b>NNBOND</b>, but that can lead to
overly large arrays dimensions beyond a value of 4. Current default value is 4 and that should work for almost all systems as the larger value of
<b>NNBOND</b> is there mainly for small molecule ions.
</li>
<li><b><a name="SMALLEST">SMALLEST</a></b> a value close to the smallest double precision number a computer can handle.
This is usually set to 1d-300. There is no reason to adjust this unless your machine can handle significantly smaller numbers.
</li>
<li><b><a name="MAXPBOX">MAXPBOX</a></b> maximum number of simulation box combinations for the volume moves.
Currently set as a function of MAXBOX.
</li>
<li><b><a name="MAXTOR">MAXTOR</a></b> maximum number torsions originating from any single atom. Currently set as a function of NNBOND.</li>
<li><b><a name="MAXBEND">MAXBEND</a></b> maximum number angles originating from any single atom. Currently set as a function of NNBOND.</li>
<li><b><a name="MAXAA">MAXAA</a></b> maximum number of angle-angle terms originating from any single atom. Currently set as a function of NNBOND.</li>
<li><b><a name="MAXIMPROP">MAXIMPROP</a></b> maximum number of improper torsion terms originating from any single atom.
Currently set as a function of NNBOND.
</li>
<li><b><a name="MAXOF">MAXOF</a></b> maximum number of special one-five terms originating from any single atom.
Currently set as a function of NNBOND.
</li>
<li><b><a name="MAXDIRLENGTH">MAXDIRLENGTH</a></b> maximum number of characters in the directory length.
This is used with some of the parallel features.
</li>
<li><b><a name="MAXIMPLICITTYPE">MAXIMPLICITTYPE</a></b> maximum number of types of atoms for the implicit force fields.</li>
<li><b><a name="MAXPIVOTBIN">MAXPIVOTBIN</a></b> maximum number of bins for the pivot bookkeeping.</li>
<li><b><a name="NDUMPHIST">NDUMPHIST</a></b> maximum allowable number of histogram computations before an output to file.</li>
<li><b><a name="MAXBAPROP">MAXBAPROP</a></b> maximum number of properties to average using the block averages routine.</li>
<li><b><a name="MAX_FOREIGN_LAMBDA">MAX_FOREIGN_LAMBDA</a></b> maximum number of (lambda_lj,lambda_c) pairs for which energy evaluations will
take place. Relevant only for Scaled Lennard-Jones classical potential.
</li>
<li><b>Pound define aliases</b> the remainder of this file contains a series of variables that are pound defined to be integers. This allows us
to use sensible variables to describe things like classical potential styles, but still have the computational expediency of integer compares
versus the relative expense of character string compares.
</li>
</ul>
<li><b><a name="globalc.h">globalc.h</a></b>
<dt>contains all of the global variables for the C portion of the code.</dt>
</li>
</ul>
<b>The .F files</b>
<ul>
The bulk of Towhee is written in a slightly enhanced FORTRAN 77. All of the FORTRAN subroutines and functions end with .F and they also contain
preprocessor directives. All modern FORTRAN 77 compilers that I have tried are capable of handling the slight enhancements to standard FORTRAN 77
that are used in Towhee. Below I list all of the .F files that are in Towhee. These are broken up into several different classes of
subroutines/functions in order to make it easier to follow the logic of the code.
<dt><font color="red">Main program</font>
<ul>
<li><a name="mainloop.F"><b>mainloop.F</b>: this subroutine is the main control of the towhee code. It calls readinput to read in the input files.
It initializes many of the statistics and safety features, and it determines which move to perform each step, and then calls the appropriate move
subroutine. It also prints out most of the measured quantities at the end of the simulation.</a>
</li>
</ul>
<dt><font color="red">Input and Initialization</font>
<ul>
<li><a name="readinput.F"><b>readinput.F</b>: this subroutine opens the towhee_input and towhee_altinp files. It then reads in the
<b>inputformat</b> variable from towhee_input. This variable determines whether to call readtowhee, readlammps, or readdatabase.</a>
</li>
<li><a name="readtowhee.F"><b>readtowhee.F</b>: this subroutine reads in the data from towhee_input and towhee_initial. It calls the other
input routines if they are needed, it calls the force field routines to initialize parameters, and it performs some error checking. If the
code stops before performing any Monte Carlo moves, then readinput is the first place to check.</a>
</li>
<li><a name="rwcbmc.F"><b>rwcbmc.F</b>: this subroutine reads in from towhee_input or write out to towhee_altinp all of the variables related
to the configurational-bias Monte Carlo move settings.</a>
</li>
<li><a name="readlammps.F"><b>readlammps.F</b>: this subroutine reads information from the lammps_input and lammps_data files in order to create
towhee files for use in a Towhee simulation run. This subroutine outputs lammps_coords_## files, a towhee_altinp file, and a towhee_ff file.</a>
</li>
<li><a name="rwforcefield.F"><b>rwforcefield.F</b>: this subroutine either reads or writes all of the force field information to towhee_ff.</a></li>
<li><a name="readclassical.F"><b>readclassical.F</b>: this subroutine reads all of the variables that are required when <b>potentialstyle</b>
is 'classical'</a>
</li>
<li><a name="readquantum.F"><b>readquantum.F</b>: this subroutine reads all of the variables that are required when <b>potentialstyle</b>
is 'quantum'</a>
</li>
<li><a name="setpotentiallogic.F"><b>setpotentiallogic.F</b>: this subroutine sets up all of logicals that determine which additional terms are
read or written for each kind of <b>classical_potential</b></a>
</li>
<li><a name="buildhelix.F"><b>buildhelix.F</b>: this subroutine constructs a helical initial configuration using the helix_keyatom and then uses
configurational-bias to grow in the rest of the atoms.</a>
</li>
<li><a name="helixpos.F"><b>helixpos.F</b>: this subroutine returns a position on a helix.</a></li>
<li><a name="buildmolec.F"><b>buildmolec.F</b>: this subroutine constructs the molecule information arrays for any molecule that has an inpstyle
of 2. It reads in all of the data for those molecules, and then calls assemble to put everything together.</a>
</li>
<li><a name="buildna.F"><b>buildna.F</b>: this subroutine constructs the molecules information arrays for any molecule that has an inpstyle of 3.
It read in all of the data for those molecules, constructs a map of atom names and vibrations using the various polyxxx.F routines,
and then calls assemble to put everything together.</a>
</li>
<li><a name="buildnanotube.F"><b>buildnanotube.F</b>: this subroutine constructs an initial nanotube conformation and also assigns all of the
bonded terms needed to construct a nanotube molecule. This is called when using inpstyle 4.</a>
</li>
<li><a name="buildprot.F"><b>buildprot.F</b>: this subroutine constructs the molecules information arrays for any molecule that has an
inpstyle of 1. It read in all of the data for those molecules, constructs a map of atom names and vibrations using the various polyxxx.F routines,
and then calls assemble to put everything together.</a>
</li>
<li><a name="polyamber96.F"><b>polyamber96.F</b>: this subroutine contains templates for the amino acids for use with the Amber96 force field.
This routine is called by buildprot.F</a>
</li>
<li><a name="polyc19eef.F"><b>polyc19eef.F</b>: this subroutine contains templates for the amino acids for use with the C19eef force field.
This routine is called by buildprot.F</a>
</li>
<li><a name="polycharmm19.F"><b>polycharmm19.F</b>: this subroutine contains templates for the amino acids for use with the Charmm19 force field.
This routine is called by buildprot.F</a>
</li>
<li><a name="polycharmm22.F"><b>polycharmm22.F</b>: this subroutine contains templates for the amino acids for use with the Charmm22 force field.
This routine is called by buildprot.F</a>
</li>
<li><a name="polycharmm27.F"><b>polycharmm27.F</b>: this subroutine contains templates for the amino acids for use with the Charmm27 force field.
This routine is called by buildprot.F.</a>
</li>
<li><a name="polycharmm27.F"><b>polycharmm27na.F</b>: this subroutine contains templates for the nucleic acids for use with the Charmm27 force
field. This routine is called by buildna.F.</a>
</li>
<li><a name="polysafetycheck.F"><b>polysafetycheck.F</b>: this subroutine checks to see if there is enough memory left in the molecule template
arrays for the requested new atoms when building molecules using the poly*.F routines.</a>
</li>
<li><a name="monomers.F"><b>monomers.F</b>: contains shared information for each monomer that is used in the poly*.F routines.</a></li>
<li><a name="assemble.F"><b>assemble.F</b>: this subroutine takes atom names and a vibration map and determines all of the parameters needed for
atoms, vibrations, bending angles, regular torsions, and angle-angle terms. It also determines the type of any improper torsion interactions.</a>
</li>
<li><a name="createmolecule.F"><b>createmolecule.F</b>: this subroutine is used with the readlammps functionality. This takes the connectivity
map generated in readlammps and turns it into the molecule data structures needed for Towhee.</a>
</li>
<li><a name="comparestruc.F"><b>comparestruc.F</b>: this subroutine is used with the readlammps functionality. It compares two molecule data
structures to see if they are identical.</a>
</li>
<li><a name="getelement.F"><b>getelement.F</b>: this subroutine is used with the readlammps functionality. This takes an elemental mass read in
by readlammps and turns it into an element name for use with the pdb writer.</a>
</li>
<li><a name="fffield.F"><b>fffield.F</b>: this subroutine sets up all of the parameters needed for the external fields.</a></li>
<li><a name="setmixterms.F"><b>setmixterms.F</b>: this subroutine sets up all of nonbonded cross terms according to the mixing rule. It also
converts all of the angles into radians.</a>
</li>
<li><a name="checkstruc.F"><b>checkstruc.F</b>: this subroutine sets up the bond-bond information, and it also performs extensive error checking
on all of the molecules to make sure that they are set up in a consistent manner.</a>
</li>
<li><a name="findrings.F"><b>findrings.F</b>: this subroutine sets up data structures that are used when performing configurational-bias on
molecules which contain cyclic moieties, or on proteins.</a>
</li>
<li><a name="initaverages.F"><b>initaverages.F</b>: this subroutine initializes all of the quantities that are tracked by the averages.F
subroutine. Called from mainloop.F</a>
</li>
<li><a name="initconf.F"><b>initconf.F</b>: this subroutine sets up an initial conformation when linit is true. Otherwise the initial
conformation is read from towhee_initial.</a>
</li>
<li><a name="initialize.F"><b>initialize.F</b>: this subroutine initializes many of the input variables. It is called from readinput before
any variable are read from the input files.</a>
</li>
</ul>
</dt>
<dt><font color="red">Monte Carlo Moves and Move Support</font>
<ul>
<li><a name="volnpt.F"><b>volnpt.F</b>: this subroutine performs a volume change move on a single box and the move is accepted based on the
energy change, number density, and the specified external pressure. The molecule positions are all scaled based upon their centers of mass
so there are no changes to the bonded energies, although the intramolecular energy could change if you are using periodic boundary
conditions with a large molecule. Note that you cannot use this move with a molecule that is bonded through the periodic boundary condition
(like a zeolite).</a>
</li>
<li><a name="volnvt.F"><b>volnvt.F</b>: this subroutine performs a volume change move on pair of boxes the move is accepted based on the energy
change and the number densities. The molecule positions are all scaled based upon their centers of mass so there are no changes to the bonded
energies, although the intramolecular energy could change if you are using periodic boundary conditions with a large molecule.
Note that you cannot use this move with a molecule that is bonded through the periodic boundary condition (like a zeolite).</a>
</li>
<li><a name="updatevolmaxdisp.F"><b>updatevolmaxdisp.F</b>: this subroutine periodically update the maximum volume displacements in an attempt
to achieve the target acceptance rate set by the user.
</li>
<li><a name="swapmoves.F"><b>swapmoves.F</b>: this subroutine performs all of the molecule swap moves. This includes 2-box configurational-bias
molecule transfer, 1-box configurational-bias molecule reinsertion, 2-box rotational-bias molecule transfer, and the aggregation-volume-bias
moves.
</li>
<li><a name="cbregrow.F"><b>cbregrow.F</b>: this subroutine performs a configurational-bias molecule regrowth move. This is different from
the intrabox molecule transfer move because at least one atom of the target molecule remains in the same location. This subroutine performs
either the standard regrowth (pmcb), or a special backbone regrowth move (pmback) using the
<a href="cbmc.html">configurational-bias</a> algorithm.</a>
</li>
<li><a name="conrot.F"><b>conrot.F</b>: this subroutine performs a concerted rotation move. This move is designed to change the torsional
conformation of several interior atoms simultaneously while keeping the bond lengths and bending angles constant.</a>
</li>
<li><a name="initloopclosure.F"><b>initloopclosure.F</b>: this subroutine initializes the variables used in a concerted rotation move.</a></li>
<li><a name="loopclosure.F"><b>loopclosure.F</b>: this subroutine performs the loop closure for the concerted rotation move.</a></li>
<li><a name="pivot.F"><b>pivot.F</b>: this subroutine performs the pivot move. This move is designed to rotate part of the molecule around
a single torsional bond.</a>
</li>
<li><a name="atomshift.F"><b>atomshift.F</b>: this subroutine performs the plane-shift and row-shift moves. These moves are designed to move
groups of molecules at the same time.</a>
</li>
<li><a name="tranatom.F"><b>tranatom.F</b>: this subroutine performs a translation move (in a random direction) upon one randomly selected atom
of a molecule. The move is accepted based upon the energy change. This move is useful for large networked molecules (like zeolites),
or for large molecules for which the configurational-bias moves have a low acceptance rate (like proteins).</a>
</li>
<li><a name="trancom.F"><b>trancom.F</b>: this subroutine attempts to move an entire molecule in a random direction. The move is accepted based
upon the energy change.</a>
</li>
<li><a name="rotate.F"><b>rotate.F</b>: this subroutine attempts to rotate a molecule about a random axis that runs through the center of mass
of the molecule. This move will not work properly for a molecule that is bonded through the periodic boundaries (like zeolites). The move
is accepted based upon the energy change.</a>
</li>
<li><a name="updatetrmaxdisp.F"><b>updatetrmaxdisp.F</b>: this subroutine periodically updates the maximum translation and rotation values in
an attempt to achieve the target acceptance rate set in towhee_input.
</li>
<li><a name="reseteamrho.F"><b>reseteamrho.F</b>: this subroutine sets the EAM densities to the new values when a move is accepted using the
Embedded Atom Method potential.</a>
</li>
<li><a name="resetewald.F"><b>resetewald.F</b>: this subroutine sets the Ewald sum parameters either at the beginning of the simulation, or when
a volume change is attempted.</a>
</li>
</ul>
</dt>
<dt><font color="red">Configurational-bias support routines</font>
<ul>
<li><a name="schedule.F"><b>schedule.F</b>: this subroutine sets up the growth schedule for all of the moves that use the
<a href="cbmc.html">configurational-bias</a> algorithm. This is the heart of the logic that controls the configurational-bias moves so you
should be very careful about making changes in this subroutine.</a>
</li>
<li><a name="rosenbluth.F"><b>rosenbluth.F</b>: this subroutine is the main control for all of the moves that use the
<a href="cbmc.html">configurational-bias</a> algorithm. It grows either the new or old conformation of the molecule according to the plan
determined in schedule.</a>
</li>
<li><a name="getcbbond.F"><b>getcbbond.F</b>: this subroutine constructs the bond lengths during a configurational-bias move.</a></li>
<li><a name="getcbangle.F"><b>getcbangle.F</b>: this subroutine constructs the bond bending angles during a configurational-bias move.</a></li>
<li><a name="getcbdihed.F"><b>getcbdihed.F</b>: this subroutine constructs the dihedral angles during a configurational-bias move.</a></li>
<li><a name="setcbdihed.F"><b>setcbdihed.F</b>: this subroutine constructs the logic needed to generate dihedral angles during a
configurational-bias move.</a>
</li>
<li><a name="dihedral_distribution.F"><b>dihedral_distribution.F</b>: this subroutine generates the dihedral trial conformations according to
the appropriate arbitrary trial distribution.
</li>
<li><a name="getweight.F"><b>getweight.F</b>: this subroutine turns a trial energy into a Rosenbluth weight. It makes sure that the weight
returned does not go below machine precision by returning the weight as an integer scale factor and a double precision residual weight.</a>
</li>
<li><a name="resetcbmc.F"><b>resetcbmc.F</b>: this subroutine resets all of the energy and weight variables at the start of a cbmc or
rotational-bias move.</a>
</li>
<li><a name="cone.F"><b>cone.F</b>: this subroutine is used to convert between Cartesian coordinates and spherical coordinates.</a></li>
<li><a name="coneangle.F"><b>coneangle.F</b>: this subroutine takes two unit vectors in spherical coordinates and computes the angle between
them.</a>
</li>
<li><a name="sphere.F"><b>sphere.F</b>: this subroutine randomly generates a unit vector on the unit sphere.</a></li>
<li><a name="gaussian.F"><b>gaussian.F</b>: this function returns a number from a specified gaussian distribution.</a></li>
<li><a name="gaussprob.F"><b>gaussprob.F</b>: this function returns the probability density for taking a number from a specified gaussian
distribution.</a>
</li>
<li><a name="febias.F"><b>febias.F</b>: this function computes the bias that is used when performing a fixed-endpoint configurational-bias
move.</a>
</li>
<li><a name="findtarget.F"><b>findtarget.F</b>: this subroutine finds a target molecule for all of the swapmoves when they need to find a
molecule that is in a certain region of space.</a>
</li>
<li><a name="rotationmatrix.F"><b>rotationmatrix.F</b>: this subroutine performs a rotation about the x, y, and z axes. This is used with
both the rotation move, and with the rotational-bias move.</a>
</li>
<li><a name="updatetwobondbias.F"><b>updatetwobondbias.F</b>: this subroutine periodically updates the variables associated with self-adapting
two-bond fixed-endpoint biasing.
</li>
<li><a name="updatethreebondbias.F"><b>updatethreebondbias.F</b>: this subroutine periodically updates the variables associated with self-adapting
three-bond fixed-endpoint biasing.
</li>
</ul>
</dt>
<dt><font color="red">Energy and Pressure Routines</font>
<ul>
<li><a name="engtotal.F"><b>engtotal.F</b>: this subroutine computes the total energy for one of the simulation boxes. There is a special option
for volume move calls to this routine that computes the total energy, except for the bonded intramolecular terms. All nonbonded inter- and
intra-molecular terms are computed.</a>
</li>
<li><a name="energy_change.F"><b>energy_change.F</b>: the subroutines in this file compute the energy change of a subset of atoms or molecules
with the rest of the system.</a>
</li>
<li><a name="energy.F"><b>energy.F</b>: this subroutines in this file compute the energy of a subset of atoms or molecules with the rest of the
system.</a>
</li>
<li><a name="engatom.F"><b>engatom.F</b>: this subroutine computes the energy of a list of atoms with the rest of the atoms in one simulation box.
This is used with the configurational-bias moves.</a>
</li>
<li><a name="bondorder.F"><b>bondorder.F</b>: this subroutine computes the bond order for use with multibody force fields.</a></li>
<li><a name="vbond.F"><b>vbond.F</b>: this function computes a single bond vibration energy.</a></li>
<li><a name="vbonbon.F"><b>vbonbon.F</b>: this function computes a single Class 2 bond-bond energy.</a></li>
<li><a name="vangle.F"><b>vangle.F</b>: this function computes a single bending angle energy.</a></li>
<li><a name="vangang.F"><b>vangang.F</b>: this function computes a single Class 2 angle-angle energy.</a></li>
<li><a name="vcoulomb.F"><b>vcoulomb.F</b>: this function computes real-space coulombic energy between two atoms.</a></li>
<li><a name="vfield.F"><b>vfield.F</b>: this function computes the interaction energy of an atom with all of the external fields.</a></li>
<li><a name="vimproper.F"><b>vimproper.F</b>: this function computes an improper torsion energy.</a></li>
<li><a name="vtorsion.F"><b>vtorsion.F</b>: this function computes a regular torsion energy.</a></li>
<li><a name="vtwobody.F"><b>vtwobody.F</b>: this function computes the van der Waals energy between two atoms.</a></li>
<li><a name="vthreebody.F"><b>vthreebody.F</b>: this function computes a three-body term between three atoms which are not bonded to each other
but interact via a three body force field</a>
</li>
<li><a name="vembed.F"><b>vembed.F</b>: this function computes the embedding energy for the EAM potential</a></li>
<li><a name="veefone.F"><b>veefone.F</b>: this function computes the solvation energy using the EEF1 implicit solvent.</a></li>
<li><a name="vsasa.F"><b>vsasa.F</b>: this function computes the solvation energy using the SASA implicit solvent.</a></li>
<li><a name="fielddft.F"><b>fielddft.F</b>: this subroutine controls the computation of the solvation free energies using the molecular
density functional theory program Tramonto.</a>
</li>
<li><a name="stresstensor.F"><b>stresstensor.F</b>: this subroutine computes the stress tensor and pressure in a simulation box.</a></li>
<li><a name="wtwobody.F"><b>wtwobody.F</b>: this subroutine computes the intermolecular pair virial function divided by r<sup>2</sup> as defined
by equation 2.60 in <a href="../references.html#allen_and_tildesley">Allen and Tildesley</a></a>
</li>
<li><a name="recip.F"><b>recip.F</b>: this subroutine updates the stored sums that are used to reduce the cost of the Ewald sum for single
molecule moves.</a>
</li>
<li><a name="recippress.F"><b>recippress.F</b>: this subroutine computes the reciprocal space contribution to the pressure using the Ewald
sum</a>
</li>
<li><a name="recipsum.F"><b>recipsum.F</b>: this subroutine computes the reciprocal space portion of the Ewald sum for an entire simulation
box.</a>
</li>
<li><a name="tail.F"><b>tail.F</b>: this subroutine calculates the values needed to compute analytical tail corrections to the energy and
pressure.</a>
</li>
<li><a name="interpolate.F"><b>interpolate.F</b>: this file contains several functions that interpolate the cubic splines used with the embedded
atom potential.</a>
</li>
<li><a name="spline.F"><b>spline.F</b>: this subroutine sets up the cubic splines that are used in the lookup tables for the embedded-atom
potential.</a>
</li>
</ul>
</dt>
<dt><font color="red">Output and Averages</font>
<ul>
<li><a name="averages.F"><b>averages.F</b>: this subroutine keeps track of the data structures used to perform the regular and block averaging
during the simulation.</a>
</li>
<li><a name="accumulateaverages.F"><b>accumulateaverages.F</b>: this subroutine controls the averaging operations that occur at the end each
move.</a>
</li>
<li><a name="pupdate.F"><b>pupdate.F</b>: this subroutine controls the averaging operations that occur at the end of a block.</a></li>
<li><a name="openfile.F"><b>openfile.F</b>: this subroutine opens up a file in the appropriate directory.</a></li>
<li><a name="rwconf.F"><b>rwconf.F</b>: this subroutine either inputs a configuration file from towhee_initial or outputs a configuration
file to either towhee_backup or towhee_final.</a>
</li>
<li><a name="writeaverages.F"><b>writeaverages.F</b>: this subroutine outputs all of the total average and block average information at the
end of the run.</a>
</li>
<li><a name="writedynamo.F"><b>writedynamo.F</b>: this subroutine outputs the embedded atom method potential using the dynamo format.</a></li>
<li><a name="writeintro.F"><b>writeintro.F</b>: this subroutine outputs information about the Towhee project and the GNU public license at the
start of the run. Called by mainloop.F.</a>
</li>
<li><a name="writelammps.F"><b>writelammps.F</b>: this subroutine outputs files of the final configuration that are suitable for use as inputs
to the molecular dynamics code <a href="http://lammps.sandia.gov/">LAMMPS</a>.</a>
</li>
<li><a name="writemovie.F"><b>writemovie.F</b>: this subroutine outputs snapshots of the simulation to the towhee_movie file for later analysis
with the analyse_movie utility.</a>
</li>
<li><a name="writepdb.F"><b>writepdb.F</b>: this subroutine outputs files of the final configuration in the pdb format. These are useful for
visualization of the simulation using a tool such as <a href="http://www.umass.edu/microbio/rasmol/">RasMol</a>.</a>
</li>
<li><a name="writeruntime.F"><b>writeruntime.F</b>: this subroutine writes run-time information to standard output with a frequency that is set
by the <b>printfreq</b> variable.
</li>
<li><a name="writetowhee.F"><b>writetowhee.F</b>: this subroutine outputs the towhee_altinp file. This file is suitable for use as a
towhee_input file in subsequent simulations.</a>
</li>
<li><a name="writetramonto.F"><b>writetramonto.F</b>: this subroutine outputs files of the final configuration that are suitable for use as
inputs to the classical density functional code Tramonto.</a>
</li>
<li><a name="writeangang.F"><b>writeangang.F</b>: this subroutine outputs all of the constants for all of the angle-angle terms used in the
simulation.</a>
</li>
<li><a name="writeangle.F"><b>writeangle.F</b>: this subroutine outputs all of the constants for all of the angle terms used in the
simulation.</a>
</li>
<li><a name="writebond.F"><b>writebond.F</b>: this subroutine outputs all of the constants for all of the bond terms used in the simulation.</a></li>
<li><a name="writeimproper.F"><b>writeimproper.F</b>: this subroutine outputs all of the constants for all of the improper torsion terms used
in the simulation.</a>
</li>
<li><a name="writetorsion.F"><b>writetorsion.F</b>: this subroutine outputs all of the constants for all of the regular torsion terms used in
the simulation.</a>
</li>
<li><a name="writenonbond.F"><b>writenonbond.F</b>: this subroutine outputs the constants for all of the nonbonded terms used in the
simulation.</a>
</li>
</ul>
</dt>
<dt><font color="red">Global Data, Coordinates and Periodic Boundaries</font>
<ul>
<li><a name="arbtocart.F"><b>arbtocart.F</b>: transforms from the arbitrary coordinate system (based on the hmatrix) into the Cartesian coordinate
system.</a>
</li>
<li><a name="carttoarb.F"><b>carttoarb.F</b>: transforms from the Cartesian coordinate system into the arbitrary coordinate system.</a></li>
<li><a name="checkhmatrix.F"><b>checkhmatrix.F</b>: checks to make sure that all three vectors of the hmatrix have an angle of at least 45 degrees
between them. This is needed as a safety check on the simplified version of the minimum image convention.</a>
</li>
<li><a name="inverthmatrix.F"><b>inverthmatrix.F</b>: inverts the hmatrix and computes the boxvolume. The inverse hmatrix is used to transform
between the Cartesian and arbitrary coordinate systems.</a>
</li>
<li><a name="getnbtype.F"><b>getnbtype.F</b>: this subroutine determines the array index for the interactions between two types of atoms.</a></li>
<li><a name="globaldata.F"><b>globaldata.F</b>: this file contains many subroutines that contain the global data structures
with localized data that is accessed via subroutine calls.</a>
</li>
<li><a name="globalaccess.F"><b>globalaccess.F</b>: this file contains functions and subroutines that make it easier to access the data
structures that are now contained in globaldata.F.</a>
</li>
<li><a name="mimage.F"><b>mimage.F</b>: this subroutine enforces the minimum image convention on a set of distances.</a></li>
<li><a name="minboxlength.F"><b>minboxlength.F</b>: this subroutine returns the minimum box length.</a></li>
<li><a name="maxboxlength.F"><b>maxboxlength.F</b>: this subroutine returns the maximum box length.</a></li>
<li><a name="putarbinbox.F"><b>putarbinbox.F</b>: this subroutine takes a set of arbitrary coordinates and puts them back into the central
box image.</a>
</li>
<li><a name="putcartinbox.F"><b>putcartinbox.F</b>: this subroutine takes a set of Cartesian coordinates and puts them back into the central
box image.</a>
</li>
<li><a name="uniformbox.F"><b>uniformbox.F</b>: this subroutine generates the Cartesian coordinates of an atom that is selected uniformly from
the entire central simulation box.</a>
</li>
</ul>
</dt>
<dt><font color="red">Force Field Fitting and Database Routines</font>
<ul>
<li><a name="readdatabase.F"><b>readdatabase.F</b>: this subroutine reads information from the database_input date file and evaluates the
database of structures against a trial force field. It is also capable of some simple optimization.</a>
</li>
<li><a name="leastsquares.F"><b>leastsquares.F</b>: this subroutine performs a least squares fit on the arrays passed into it.</a></li>
<li><a name="sdb_config.F"><b>sdb_config.F</b>: one of the support subroutines for parsing the sdb database format.</a></li>
<li><a name="sdb_rdstruct.F"><b>sdb_rdstruct.F</b>: one of the support subroutines for parsing the sdb database format.</a></li>
<li><a name="sdb_rdtoend.F"><b>sdb_rdtoend.F</b>: one of the support subroutines for parsing the sdb database format.</a></li>
<li><a name="sdb_strget.F"><b>sdb_strget.F</b>: one of the support subroutines for parsing the sdb database format.</a></li>
<li><a name="sdb_strpars.F"><b>sdb_strpars.F</b>: one of the support subroutines for parsing the sdb database format.</a></li>
</ul>
</dt>
<dt><font color="red">Other Routines</font>
<ul>
<li><a name="arccos.F"><b>arccos.F</b>: this is a safe implementation of the standard FORTRAN function dacos. It does not crash when taking
the anti-cosine of a number that is just a bit larger than 1.0 or a bit smaller than -1.0.</a>
</li>
<li><a name="crossproduct.F"><b>crossproduct.F</b>: this subroutine computes the cross product of two vectors.</a></li>
<li><a name="ctrmas.F"><b>ctrmas.F</b>: this subroutine computes the center-of-mass of molecules and also the maximum distance from any atom
to the center-of-mass.</a>
</li>
<li><a name="distance.F"><b>distance.F</b>: this function computes the distance given a three dimensional vector.</a></li>
<li><a name="dotproduct.F"><b>dotproduct.F</b>: this function computes the normalized dot product of two vectors.</a></li>
<li><a name="expon.F"><b>expon.F</b>: this function computes exponential of a number in a safe way so that if the value inside the exponential
would result in a number that is less than SMALLEST, the function instead returns zero. Thus, this function will never result in an underflow
error, although an overflow is still possible as there are other checks in the code to prevent an overflow.</a>
</li>
<li><a name="internal.F"><b>internal.F</b>: this file contains subroutines that are normally handled by intrinsic functions, but occasionally
need explicit support on machines that do not have the appropriate intrinsic libraries.
</li>
<li><a name="linclude.F"><b>linclude.F</b>: this file contains a subroutine (setinclude) and a function (linclude) which are used to determine
if two atoms on the same molecule have nonbonded interactions.</a>
</li>
<li><a name="minimizer.F"><b>minimizer.F</b>: this subroutine performs a minimization of the coordinates and box dimensions.</a></li>
<li><a name="problem.F"><b>problem.F</b>: this subroutine is called when there is a problem in the code and we need to exit. Currently it only
sets a logical, but in the future it will handle the graceful exit of the code during a multiprocessor simulation.</a>
</li>
<li><a name="random.F"><b>random.F</b>: a file which contains one function (random) which controls the generation of random numbers. There are
other functions and subroutines in this file which generate the random numbers.</a>
</li>
</ul>
</dt>
<dt><font color="red">forcefield Program Routines (not needed to compile towhee)</font>
<ul>
<li><b>createff.F</b>: the main driver for the forcefield program.</li>
<li><b>ffcheck.F</b>: this subroutine performs bounds checking on the force field generation routines.</li>
<li><b>ffackl2004.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/ackl2004.html">Ackland <i>et al.</i> 2004</a> force field.
</li>
<li><b>ffalavi2005.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/alavi2005.html">Alavi <i>et al.</i> 2005</a> force field.
</li>
<li><b>ffamber96.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/amber_param96.html">Amber96</a> force field.
</li>
<li><b>ffaqvist.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/aqvist.html">Aqvist</a> force field.
</li>
<li><b>ffc19eef1.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/c19eef1.html">C19eef1</a> force field.
</li>
<li><b>ffc19sasa.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/c19sasa.html">C19sasa</a> force field.
</li>
<li><b>ffcatlowfaux.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/catlow_faux.html">CatlowFaux</a> force field.
</li>
<li><b>ffcharmm19.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/charmm19.html">Charmm19</a> force field.
</li>
<li><b>ffc27rigid.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/c27rigid.html">C27rigid</a> force field.
</li>
<li><b>ffcharmm22.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/charmm22.html">Charmm22</a> force field.
</li>
<li><b>ffcharmm22fe.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/charmm22fe.html">Charmm22fe</a> supplemental force field.
</li>
<li><b>ffcharmm27.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/charmm27.html">Charmm27</a> force field.
</li>
<li><b>ffcharmm27x.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/charmm27x.html">Charmm27x</a> force field supplement.
</li>
<li><b>ffclayff.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/clayff.html">ClayFF</a> force field.
</li>
<li><b>ffcompass.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/compass.html">COMPASSv1</a> force field.
</li>
<li><b>ffcoon1987.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/coon1987.html">Coon1987</a> force field.
</li>
<li><b>ffcui1998.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/cui1998.html">Cui <i>et al.</i> 1998</a> force field.
</li>
<li><b>ffcui2002.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/cui2002.html">Cui and Elliott 2002</a> force field.
</li>
<li><b>ffdacnisua.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/dacnisua.html">DACNIS-UA</a> force field.
</li>
<li><b>ffdick1994.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/dick1994.html">Dick and Ritchie 1994</a> force field.
</li>
<li><b>ffding1986.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/ding1986.html">Ding1986</a> force field.
</li>
<li><b>ffdreiding.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/dreiding.html">DREIDING</a> force field.
</li>
<li><b>ffdubb2004.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/dubb2004.html">Dubb2004</a> force field.
</li>
<li><b>ffelli2002.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/elli2002.html">Elliott 2002</a> force field.
</li>
<li><b>ffepm.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/epm.html">EPM</a> force field.
</li>
<li><b>fffris2003.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/fris2003.html">Fris2003</a> force field.
</li>
<li><b>ffgala1994.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/gala1994.html">Gala1994</a> force field.
</li>
<li><b>ffgordon.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/gordon.html">Gordon</a> force field.
</li>
<li><b>ffgromos43a1.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/gromos43a1.html">Gromos43A1</a> force field.
</li>
<li><b>ffhardsphere.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/hardsphere.html">HardSphere</a> force field.
</li>
<li><b>ffkfvbvs.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/kfvbvs.html">KFvBvS</a> force field.
</li>
<li><b>fflast1993.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/last1993.html">Last1993</a> force field.
</li>
<li><b>fflgm.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/lgm.html">LGM</a> force field.
</li>
<li><b>ffljium.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/ljium.html">LJium</a> force field.
</li>
<li><b>ffmend2003.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/mend2003.html">Mendelev <i>et al.</i> 2003</a> force field.
</li>
<li><b>ffmgmstereo.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/mgmstereo.html">MGM stereochemistry enforcer</a> force field supplement.
</li>
<li><b>ffmm2.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/mm2.html">MM2</a> force field.
</li>
<li><b>ffmorrow2002.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/morrow2002.html">Morrow and Maginn 2002</a> force field.
</li>
<li><b>ffnerdv1.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/nerdv1.html">NERD Version 1</a> force field.
</li>
<li><b>ffnerdv2.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/nerdv2.html">NERD Version 2</a> force field.
</li>
<li><b>ffnerdv3.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/nerdv3.html">NERD Version 3</a> force field.
</li>
<li><b>ffopls2001.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/opls2001.html">OPLS-2001</a> force field.
</li>
<li><b>ffoplsaa.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/oplsaa.html">OPLS-aa</a> force field.
</li>
<li><b>ffoplsua.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/oplsua.html">OPLS-ua</a> force field.
</li>
<li><b>ffpana1989.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/pana1989.html">Panagiotopoulos 1989</a> force field.
</li>
<li><b>ffpmf.F</b>: this subroutine reads in radial distribution function and converts it into a potential of mean force tabulated potential.</li>
<li><b>ffpotter1997.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/potter1997.html">Potter <i>et al.</i> 1997</a> force field.
</li>
<li><b>ffqmff_viii.F</b>: this subroutine contains a partial implementation of the QMFF-VIII force field.</li>
<li><b>ffreadcharmmfile.F</b>: this subroutine reads in a native Charmm force field file and populates the Towhee force field data structure.</li>
<li><b>ffreadsetflfile.F</b>: this subroutine reads in an EAM setfl file and populates the Towhee force field data structure.</li>
<li><b>ffrichar1995.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/richar1995.html">Richards <i>et al.</i> 1995</a> force field.
</li>
<li><b>ffshah2004.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/shah2004.html">Shah and Maginn 2004</a> force field.
</li>
<li><b>ffshukla1987.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/shukla1987.html">Shukla 1987</a> force field.
</li>
<li><b>ffsks.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/sks.html">SKS</a> force field.
</li>
<li><b>ffsmith1994.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/smith1994.html">Smith and Dang 1994</a> force field.
</li>
<li><b>ffsmmkmain.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/smmkmain.html">SMMK main</a> force field.
</li>
<li><b>ffsmmknaip.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/smmknaip.html">SMMK Note Added in Proof</a> force field.
</li>
<li><b>ffspce.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/spce.html">SPC-E</a> force field.
</li>
<li><b>ffsquarewell.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/squarewell.html">SquareWell</a> force field.
</li>
<li><b>ffstil1985.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/stil1985.html">Stil1985</a> force field.
</li>
<li><b>ffsum2003.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/sum2003.html">Sum2003</a> force field.
</li>
<li><b>fftele1987.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/tele1987.html">Tele1987</a> force field.
</li>
<li><b>fftip3p.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/tip3p.html">TIP3P</a> force field.
</li>
<li><b>fftip4p.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/tip4p.html">TIP4P</a> force field.
</li>
<li><b>fftip5p.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/tip5p.html">TIP5P</a> force field.
</li>
<li><b>fftrappeeh.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/trappeeh.html">TraPPE-EH</a> force field.
</li>
<li><b>fftrappeua.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/trappeua.html">TraPPE-UA</a> force field.
</li>
<li><b>fftrappeuaf.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/trappeuaf.html">TraPPE-UA flexible</a> force field.
</li>
<li><b>ffuff.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/uff.html">UFF</a> force field.
</li>
<li><b>ffunlu2004.F</b>: this subroutine contains a partial implementation of the Unlu and Elliott 2004 force field.</li>
<li><b>ffvega1992.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/vega1992.html">Vega <i>et al.</i> 1992</a> force field.
</li>
<li><b>ffvink2001.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/vink2001.html">Vink2001</a> force field.
</li>
<li><b>ffwalt2001.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/walt2001.html">Walt2001</a> force field.
</li>
<li><b>ffweiner1984.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/weiner1984.html">Weiner <i>et al.</i> 1984</a> force field.
</li>
<li><b>ffweiner1986.F</b>: this subroutine sets all of the parameters needed to build the
<a href="../forcefields/weiner1986.html">Weiner <i>et al.</i> 1986</a> force field.
</li>
</ul>
</dt>
</ul>
<b>The .c files</b>
<ul>
<dt><font color="red">C routines</font>
<ul>
<li><a name="towhee.c"><b>towhee.c</b>: This is where everything begins (main). If using the MPI version of towhee this handles the
initialization of MPI and also reads from the towhee_parallel file. Otherwise it just handles the command line variables sent to Towhee and
then calls <b>mainloop.F</b>.</a>
</li>
<li><a name="control.c"><b>control.c</b>: This set of routines is used to handle some of the MPI calls and to serve as an interface between
Towhee and the Tramonto codes.</a>
</li>
<li><a name="jobfarm.c"><b>jobfarm.c</b>: This set of routines handles the MPI calls required to run a parallel simulation that farms out a list
of jobs over several processors, where each processor runs a single job at a time.</a>
</li>
<li><a name="rex.c"><b>rex.c</b>: Implementation of Replica Exchange functionality. Replica Exchange requires MPI to run. While functional, it
is currently at an early stage of development.</a>
</li>
<li><a name="sturm.c"><b>sturm.c</b>: These routines handle much of the mathematics required for the concerted rotation moves.</a></li>
</ul>
</dt>
</ul>
<b>Bug Reports</b>
<ul>
In a code of this magnitude there will invariably be bugs from time to time. Hopefully all of the big ones are out of the code, but there is
a continual process of adding features (rebugging) and testing the features (debugging). If you do find a problems with the code, please let us
know so we can fix it for the benefit of everyone who is using the program. The more detail you can provide in your bug report the better.
If you have a specific case that crashes then sending copies of the input files will greatly expedite the debugging process. We are now using the
Bug Tracking software at SourceForge. To submit a bug just head to the
<a href="https://sourceforge.net/tracker/?atid=581786&group_id=87039&func=browse">Towhee Bug Tracker</a> site and click on the "submit new" button.
The best option is for you to log into SourceForge (creating an account is free) and use that account to submit the bug, in which case it will
automatically notify you of the progress resolving the bug. Alternatively, you can send an email about your bug to
<a href="mailto:towhee-bugs@lists.sourceforge.net">towhee-bugs@lists.sourceforge.net</a>. Your posting to this list is automatically held until
we can verify it is not spam.
</ul>
<a href="../index.html">Return to the main towhee web page</a>
<p> </p>
</td>
</tr>
</table>
<hr width="715" align="left">
<i><font size="2">Send comments to:</font></i>
<font size="2">
<a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a>
<br></br>
<i>Last updated:</i>
<!-- #BeginDate format:Am1 -->November 15, 2010<!-- #EndDate -->
</font>
<br></br>
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