MCCCS Towhee: Code Manual

MCCCS Towhee: Code Manual

Overview

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 8.0.0. Compiling

autoconf Version 2.59 or later and

automake Version 1.7.4 or later

Compiling on a Unix/Linux Operating System using compilers similar to GNU

In the top level directory issue the command

./configure

cd Source

make towhee

./configure --enable-fix-GNU

Compiling on an Apple OS-X Operating System

Useful instructions and software for high performance computing on OS-X is available at http://hpc.sourceforge.net/.

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.

ld: Undefined symbols:

restFP

saveFP

make: *** [towhee] Error 1

./configure LDFLAGS=-lcc_dynamic

Compiling on a Windows 10 Operating System using the Linux Subsystem

Towhee is designed for compilation in a Unix style environment and the easiest way to get that on a Windows 10 computer is to install the linux subsystem. Microsoft has a Windows 10 linux subsystem installation guide. Once you have that running you just need to follow the usual Linux directions to install all the required compilation packages.

Compiling on a Windows Operating System using Cygwin

Towhee is designed for compilation in a Unix style environment. Previously, we suggested Windows users should utilize the freely available Cygwin software, but Windows 10 now supports a linux installation that is the suggested best option. For those still using the Cygwin environment, once you have installed Cygwin 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.

./configure

cd Source

make towhee.exe

Compiling on a Windows Operating System using Intel's Visual Fortran and Microsoft's Visual C++.

In addition to the standard towhee code, the following standard unix functionality is provided:

dirent.h : dirent API for MSVC++ (located in towhee-x.x.xx\vs_towhee\dirent)
unistd.h : a subset of the complete Unix file is used (located in towhee-x.x.xx\vs_towhee\dirent)
getopt: atgtable is an ANSI C library for parsing GNU style command line options (located in towhee-x.x.xx\vs_towhee\argtable2-12)

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.

Configure options in Towhee

./configure --enable-safe-compare
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.
./configure --enable-mpi
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 towhee_parallel manual for more information about this option.
./configure --enable-fix-GNU
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
and you are using the GNU compilers, then this option might solve your problems.
./configure --enable-internal
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.
./configure FFLAGS='-fbounds-check'
where the items between the single quotes are the flags used for the Fortran compilation.
./configure F77='pgf77' CC='pgcc'
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
./configure ADDLIB='-L/usr/whoever/lib/'
Adds user specified libraries into the link command.
./configure --enable-tramonto
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 Tramonto software link for more information.
./configure --disable-command-line-args
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.
./configure FFLAGS=''
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.

Compiling the forcefield utlitity

cd Source

make forcefield

cd /towheebase/ForceFields

/towheebase/Source/forcefield

All

The .h files

preproc.h
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.

MAXBOX 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.
NUMAX the maximum number of atoms in any molecule. Minimum value is 1. No maximum value.
NTMAX the maximum number of types of molecules in the simulation. Minimum value is 1. No maximum value.
MAXKMAX the maximum value for kmax in the Ewald sum. Minimum value is 1. No maximum value.
VECTORMAX 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 MAXKMAX.
MAXBLOCK the maximum number of blocks for the block averaging. Minimum value is 1. No maximum value.
FLDMAX the maximum number of external fields in the system. Minimum value is 1. No maximum value.
NNTYPE the maximum number of different types of atoms allowed in the simulation.
CROSSTYPEMAX the maximum number of cross types, currently set to depend upon NNTYPE.
MAXTABTYPE the maximum number of types of atoms for tabular potentials. Minimum value is 1. Maximum value is NNTYPE.
MAXTABLE the maximum number of entries to describe a tabular potential. Minimum value is 1. Maximum value is NNTYPE.
TVIBMAX the maximum number of different types of vibrations in the simulation.
TBENMAX the maximum number of different types of bending angles in the simulation.
TTORMAX the maximum number of different types of regular torsions in the simulation.
TIMPMAX the maximum number of different types of improper torsions in the simulation.
TAAMAX the maximum number of different types of angle-angle terms in the simulation.
TOFMAX the maximum number of different types of special one-five terms in the simulation.
THBONDMAX the maximum number of different types of special hydrogen bond force field terms in the simulation.
TBIMAX the maximum number of different types of bond increment terms in the simulation.
NNBOND the maximum number of bonds from any atom. Minimum value is 1. No maximum value, and currently set to a default of 6.
MMBOND 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 NNBOND, 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 NNBOND is there mainly for small molecule ions.
SMALLEST 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.
MAXPBOX maximum number of simulation box combinations for the volume moves. Currently set as a function of MAXBOX.
MAXTOR maximum number torsions originating from any single atom. Currently set as a function of NNBOND.
MAXBEND maximum number angles originating from any single atom. Currently set as a function of NNBOND.
MAXAA maximum number of angle-angle terms originating from any single atom. Currently set as a function of NNBOND.
MAXIMPROP maximum number of improper torsion terms originating from any single atom. Currently set as a function of NNBOND.
MAXOF maximum number of special one-five terms originating from any single atom. Currently set as a function of NNBOND.
MAXDIRLENGTH maximum number of characters in the directory length. This is used with some of the parallel features.
MAXIMPLICITTYPE maximum number of types of atoms for the implicit force fields.
MAXPIVOTBIN maximum number of bins for the pivot bookkeeping.
NDUMPHIST maximum allowable number of histogram computations before an output to file.
MAXBAPROP maximum number of properties to average using the block averages routine.
MAX_FOREIGN_LAMBDA maximum number of (lambda_lj,lambda_c) pairs for which energy evaluations will take place. Relevant only for Scaled Lennard-Jones classical potential.
Pound define aliases 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.

globalc.h
contains all of the global variables for the C portion of the code.

The .F files

Main program

mainloop.F: 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.

Input and Initialization

readinput.F: this subroutine opens the towhee_input and towhee_altinp files. It then reads in the inputformat variable from towhee_input. This variable determines whether to call readtowhee, readlammps, or readdatabase.
readtowhee.F: 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.
rwcbmc.F: 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.
readlammps.F: 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.
rwforcefield.F: this subroutine either reads or writes all of the force field information to towhee_ff.
readclassical.F: this subroutine reads all of the variables that are required when potentialstyle is 'classical'
setpotentiallogic.F: this subroutine sets up all of logicals that determine which additional terms are read or written for each kind of classical_potential
buildhelix.F: this subroutine constructs a helical initial configuration using the helix_keyatom and then uses configurational-bias to grow in the rest of the atoms.
helixpos.F: this subroutine returns a position on a helix.
buildmolec.F: 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.
buildna.F: 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.
buildnanotube.F: 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.
buildprot.F: 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.
polyamber96.F: this subroutine contains templates for the amino acids for use with the Amber96 force field. This routine is called by buildprot.F
polyc19eef.F: this subroutine contains templates for the amino acids for use with the C19eef force field. This routine is called by buildprot.F
polycharmm19.F: this subroutine contains templates for the amino acids for use with the Charmm19 force field. This routine is called by buildprot.F
polycharmm22.F: this subroutine contains templates for the amino acids for use with the Charmm22 force field. This routine is called by buildprot.F
polycharmm27.F: this subroutine contains templates for the amino acids for use with the Charmm27 force field. This routine is called by buildprot.F.
polycharmm27na.F: this subroutine contains templates for the nucleic acids for use with the Charmm27 force field. This routine is called by buildna.F.
polysafetycheck.F: 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.
monomers.F: contains shared information for each monomer that is used in the poly*.F routines.
assemble.F: 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.
createmolecule.F: 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.
comparestruc.F: this subroutine is used with the readlammps functionality. It compares two molecule data structures to see if they are identical.
getelement.F: 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.
setmixterms.F: this subroutine sets up all of nonbonded cross terms according to the mixing rule. It also converts all of the angles into radians.
checkstruc.F: 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.
findrings.F: this subroutine sets up data structures that are used when performing configurational-bias on molecules which contain cyclic moieties, or on proteins.
initaverages.F: this subroutine initializes all of the quantities that are tracked by the averages.F subroutine. Called from mainloop.F
initconf.F: this subroutine sets up an initial conformation when linit is true. Otherwise the initial conformation is read from towhee_initial.
initialize.F: this subroutine initializes many of the input variables. It is called from readinput before any variable are read from the input files.

Monte Carlo Moves and Move Support

volumemoves.F: these subroutines perform volume change moves on either a single box (NPT) or on a pair of simulation boxes (NVT) and the move is accepted based on the energy change, number density, and (in the NPT case) 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 currently use this move with a molecule that is bonded through the periodic boundary condition (eg cannot handle breathing modes of a flexible zeolite).
updatevolmaxdisp.F: this subroutine periodically update the maximum volume displacements in an attempt to achieve the target acceptance rate set by the user.

swapmoves.F: 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.

cbregrow.F: 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 configurational-bias algorithm.
conrot.F: 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.
initloopclosure.F: this subroutine initializes the variables used in a concerted rotation move.
loopclosure.F: this subroutine performs the loop closure for the concerted rotation move.
pivot.F: this subroutine performs the pivot move. This move is designed to rotate part of the molecule around a single torsional bond.
atomshift.F: this subroutine performs the plane-shift and row-shift moves. These moves are designed to move groups of molecules at the same time.
tranatom.F: 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).
trancom.F: this subroutine attempts to move an entire molecule in a random direction. The move is accepted based upon the energy change.
rotate.F: 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.
updatetrmaxdisp.F: this subroutine periodically updates the maximum translation and rotation values in an attempt to achieve the target acceptance rate set in towhee_input.

reseteamrho.F: this subroutine sets the EAM densities to the new values when a move is accepted using the Embedded Atom Method potential.
resetewald.F: this subroutine sets the Ewald sum parameters either at the beginning of the simulation, or when a volume change is attempted.

Configurational-bias support routines

schedule.F: this subroutine sets up the growth schedule for all of the moves that use the configurational-bias 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.
rosenbluth.F: this subroutine is the main control for all of the moves that use the configurational-bias algorithm. It grows either the new or old conformation of the molecule according to the plan determined in schedule.
getcbbond.F: this subroutine constructs the bond lengths during a configurational-bias move.
getcbangle.F: this subroutine constructs the bond bending angles during a configurational-bias move.
getcbdihed.F: this subroutine constructs the dihedral angles during a configurational-bias move.
setcbdihed.F: this subroutine constructs the logic needed to generate dihedral angles during a configurational-bias move.
dihedral_distribution.F: this subroutine generates the dihedral trial conformations according to the appropriate arbitrary trial distribution.

getweight.F: 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.
resetcbmc.F: this subroutine resets all of the energy and weight variables at the start of a cbmc or rotational-bias move.
cone.F: this subroutine is used to convert between Cartesian coordinates and spherical coordinates.
coneangle.F: this subroutine takes two unit vectors in spherical coordinates and computes the angle between them.
sphere.F: this subroutine randomly generates a unit vector on the unit sphere.
gaussian.F: this function returns a number from a specified gaussian distribution.
gaussprob.F: this function returns the probability density for taking a number from a specified gaussian distribution.
febias.F: this function computes the bias that is used when performing a fixed-endpoint configurational-bias move.
findtarget.F: 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.
rotationmatrix.F: 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.
updatetwobondbias.F: this subroutine periodically updates the variables associated with self-adapting two-bond fixed-endpoint biasing.

updatethreebondbias.F: this subroutine periodically updates the variables associated with self-adapting three-bond fixed-endpoint biasing.

atd_cbmc_setup.F: this subroutine sets up all of the arbitrarty trial distribution parameters required when using advanced CBMC growth strategies.

Energy and Pressure Routines

engtotal.F: 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.
energy_change.F: the subroutines in this file compute the energy change of a subset of atoms or molecules with the rest of the system.
energy.F: this subroutines in this file compute the energy of a subset of atoms or molecules with the rest of the system.
engatom.F: 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.
bondorder.F: this subroutine computes the bond order for use with multibody force fields.
vbond.F: this function computes a single bond vibration energy.
vbonbon.F: this function computes a single Class 2 bond-bond energy.
vangle.F: this function computes a single bending angle energy.
vangang.F: this function computes a single Class 2 angle-angle energy.
vcoulomb.F: this function computes real-space coulombic energy between two atoms.
vfield.F: this function computes the interaction energy of an atom with all of the external fields.
vimproper.F: this function computes an improper torsion energy.
vtorsion.F: this function computes a regular torsion energy.
vtwobody.F: this function computes the van der Waals energy between two atoms.
vthreebody.F: 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
vembed.F: this function computes the embedding energy for the EAM potential
veefone.F: this function computes the solvation energy using the EEF1 implicit solvent.
vsasa.F: this function computes the solvation energy using the SASA implicit solvent.
fielddft.F: this subroutine controls the computation of the solvation free energies using the molecular density functional theory program Tramonto.
stresstensor.F: this subroutine computes the stress tensor and pressure in a simulation box.
wtwobody.F: this subroutine computes the intermolecular pair virial function divided by r² as defined by equation 2.60 in Allen and Tildesley
recip.F: this subroutine updates the stored sums that are used to reduce the cost of the Ewald sum for single molecule moves.
recippress.F: this subroutine computes the reciprocal space contribution to the pressure using the Ewald sum
recipsum.F: this subroutine computes the reciprocal space portion of the Ewald sum for an entire simulation box.
tail.F: this subroutine calculates the values needed to compute analytical tail corrections to the energy and pressure.
interpolate.F: this file contains several functions that interpolate the cubic splines used with the embedded atom potential.
spline.F: this subroutine sets up the cubic splines that are used in the lookup tables for the embedded-atom potential.

Output and Averages

averages.F: this subroutine keeps track of the data structures used to perform the regular and block averaging during the simulation.
accumulateaverages.F: this subroutine controls the averaging operations that occur at the end each move.
pupdate.F: this subroutine controls the averaging operations that occur at the end of a block.
openfile.F: this subroutine opens up a file in the appropriate directory.
rwconf.F: this subroutine either inputs a configuration file from towhee_initial or outputs a configuration file to either towhee_backup or towhee_final.
writeaverages.F: this subroutine outputs all of the total average and block average information at the end of the run.
writedynamo.F: this subroutine outputs the embedded atom method potential using the dynamo format.
writeintro.F: this subroutine outputs information about the Towhee project and the GNU public license at the start of the run. Called by mainloop.F.
writelammps.F: this subroutine outputs files of the final configuration that are suitable for use as inputs to the molecular dynamics code LAMMPS.
writemovie.F: this subroutine outputs snapshots of the simulation to the towhee_movie file for later analysis with the analyse_movie utility.
writepdb.F: 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 RasMol.
writeruntime.F: this subroutine writes run-time information to standard output with a frequency that is set by the printfreq variable.

writetowhee.F: this subroutine outputs the towhee_altinp file. This file is suitable for use as a towhee_input file in subsequent simulations.
writetramonto.F: this subroutine outputs files of the final configuration that are suitable for use as inputs to the classical density functional code Tramonto.
writeangang.F: this subroutine outputs all of the constants for all of the angle-angle terms used in the simulation.
writeangle.F: this subroutine outputs all of the constants for all of the angle terms used in the simulation.
writebond.F: this subroutine outputs all of the constants for all of the bond terms used in the simulation.
writeimproper.F: this subroutine outputs all of the constants for all of the improper torsion terms used in the simulation.
writetorsion.F: this subroutine outputs all of the constants for all of the regular torsion terms used in the simulation.
writenonbond.F: this subroutine outputs the constants for all of the nonbonded terms used in the simulation.

Global Data, Coordinates and Periodic Boundaries

arbtocart.F: transforms from the arbitrary coordinate system (based on the hmatrix) into the Cartesian coordinate system.
carttoarb.F: transforms from the Cartesian coordinate system into the arbitrary coordinate system.
checkhmatrix.F: 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.
inverthmatrix.F: inverts the hmatrix and computes the boxvolume. The inverse hmatrix is used to transform between the Cartesian and arbitrary coordinate systems.
getnbtype.F: this subroutine determines the array index for the interactions between two types of atoms.
globaldata.F: this file contains many subroutines that contain the global data structures with localized data that is accessed via subroutine calls.
globalaccess.F: this file contains functions and subroutines that make it easier to access the data structures that are now contained in globaldata.F.
mimage.F: this subroutine enforces the minimum image convention on a set of distances.
minboxlength.F: this subroutine returns the minimum box length.
maxboxlength.F: this subroutine returns the maximum box length.
putarbinbox.F: this subroutine takes a set of arbitrary coordinates and puts them back into the central box image.
putcartinbox.F: this subroutine takes a set of Cartesian coordinates and puts them back into the central box image.
uniformbox.F: this subroutine generates the Cartesian coordinates of an atom that is selected uniformly from the entire central simulation box.

Other Routines

arccos.F: this is a safe implementation of the standard FORTRAN function dacos. It does not crash when taking the arc-cosine of a number that is just a bit larger than 1.0 or a bit smaller than -1.0.
crossproduct.F: this subroutine computes the cross product of two vectors.
ctrmas.F: this subroutine computes the center-of-mass of molecules and also the maximum distance from any atom to the center-of-mass.
distance.F: this function computes the distance given a three dimensional vector.
dotproduct.F: this function computes the normalized dot product of two vectors.
expon.F: 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.
internal.F: 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.

linclude.F: 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.
minimizer.F: this subroutine performs a minimization of the coordinates and box dimensions.
problem.F: 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.
random.F: 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.

forcefield Program Routines (not needed to compile towhee)

createff.F: the main driver for the forcefield program.
ffcheck.F: this subroutine performs bounds checking on the force field generation routines.
ffackl2004.F: this subroutine sets all of the parameters needed to build the Ackland et al. 2004 force field.
ffalavi2005.F: this subroutine sets all of the parameters needed to build the Alavi et al. 2005 force field.
ffamber96.F: this subroutine sets all of the parameters needed to build the Amber96 force field.
ffaqvist.F: this subroutine sets all of the parameters needed to build the Aqvist force field.
ffbelash2006.F: this subroutine sets all of the parameters needed to build the Belashchenko 2006 force field.
ffbelash2013.F: this subroutine sets all of the parameters needed to build the Belashchenko 2013 force field.
ffc19eef1.F: this subroutine sets all of the parameters needed to build the C19eef1 force field.
ffc19sasa.F: this subroutine sets all of the parameters needed to build the C19sasa force field.
ffc27rigid.F: this subroutine sets all of the parameters needed to build the C27rigid force field.
ffcatlowfaux.F: this subroutine sets all of the parameters needed to build the CatlowFaux force field.
ffcharmm19.F: this subroutine sets all of the parameters needed to build the Charmm19 force field. For an unknown reason the manual page for Charmm19 is currently missing.
ffcharmm22.F: this subroutine sets all of the parameters needed to build the Charmm22 force field.
ffcharmm22fe.F: this subroutine sets all of the parameters needed to build the Charmm22fe supplemental force field.
ffcharmm27.F: this subroutine sets all of the parameters needed to build the Charmm27 force field.
ffcharmm27x.F: this subroutine sets all of the parameters needed to build the Charmm27x force field supplement.
ffclayff.F: this subroutine sets all of the parameters needed to build the ClayFF force field.
ffcompass.F: this subroutine sets all of the parameters needed to build the COMPASSv1 force field.
ffcoon1987.F: this subroutine sets all of the parameters needed to build the Coon1987 force field.
ffcui1998.F: this subroutine sets all of the parameters needed to build the Cui et al. 1998 force field.
ffcui2002.F: this subroutine sets all of the parameters needed to build the Cui and Elliott 2002 force field.
ffdacnisua.F: this subroutine sets all of the parameters needed to build the DACNIS-UA force field.
ffdick1994.F: this subroutine sets all of the parameters needed to build the Dick and Ritchie 1994 force field.
ffding1986.F: this subroutine sets all of the parameters needed to build the Ding1986 force field.
ffdreiding.F: this subroutine sets all of the parameters needed to build the DREIDING force field.
ffdubb2004.F: this subroutine sets all of the parameters needed to build the Dubb2004 force field.
ffelli2002.F: this subroutine sets all of the parameters needed to build the Elliott 2002 force field.
ffepm.F: this subroutine sets all of the parameters needed to build the EPM force field.
fffris2003.F: this subroutine sets all of the parameters needed to build the Fris2003 force field.
fffris2008.F: this subroutine sets all of the parameters needed to build the Fris2008 force field.
ffgala1994.F: this subroutine sets all of the parameters needed to build the Gala1994 force field.
ffgordon.F: this subroutine sets all of the parameters needed to build the Gordon force field.
ffgromos43a1.F: this subroutine sets all of the parameters needed to build the Gromos43A1 force field.
ffhardsphere.F: this subroutine sets all of the parameters needed to build the HardSphere force field.
ffhoyt2003.F: this subroutine sets all of the parameters needed to build the Hoyt et al. 2003 force field.
ffjaramillo.F: this subroutine sets all of the parameters needed to build the Jaramillo et al. 2001 force field.
ffkbff.F: this subroutine sets all of the parameters needed to build the Kirkwood-Buff force field.
ffkfvbvs.F: this subroutine sets all of the parameters needed to build the KFvBvS force field.
fflast1993.F: this subroutine sets all of the parameters needed to build the Last1993 force field.
fflgm.F: this subroutine sets all of the parameters needed to build the LGM force field.
ffljium.F: this subroutine sets all of the parameters needed to build the LJium force field.
ffmcy1976.F: this subroutine sets all of the parameters needed to build the MCY 1976 force field.
ffmend2003.F: this subroutine sets all of the parameters needed to build the Mendelev et al. 2003 force field.
ffmgmstereo.F: this subroutine sets all of the parameters needed to build the MGM stereochemistry enforcer force field supplement.
ffmm2.F: this subroutine sets all of the parameters needed to build the MM2 force field.
ffmmff94.F: this subroutine sets all of the parameters needed to build the MMFF94 force field.
ffmorrow2002.F: this subroutine sets all of the parameters needed to build the Morrow and Maginn 2002 force field.
ffnerdv1.F: this subroutine sets all of the parameters needed to build the NERD Version 1 force field.
ffnerdv2.F: this subroutine sets all of the parameters needed to build the NERD Version 2 force field.
ffnerdv3.F: this subroutine sets all of the parameters needed to build the NERD Version 3 force field.
ffopls1996.F: this subroutine sets all of the parameters needed to build the OPLS-1996 force field.
ffopls2001.F: this subroutine sets all of the parameters needed to build the OPLS-2001 force field.
ffoplsaa.F: this subroutine sets all of the parameters needed to build the OPLS-aa force field.
ffoplsua.F: this subroutine sets all of the parameters needed to build the OPLS-ua force field.
ffpana1989.F: this subroutine sets all of the parameters needed to build the Panagiotopoulos 1989 force field.
ffpmf.F: this subroutine reads in radial distribution function and converts it into a potential of mean force tabulated potential.
ffpotter1997.F: this subroutine sets all of the parameters needed to build the Potter et al. 1997 force field.
ffqmff_viii.F: this subroutine contains a partial implementation of the QMFF-VIII force field.
ffreadcharmmfile.F: this subroutine reads in a native Charmm force field file and populates the Towhee force field data structure.
ffreadsetflfile.F: this subroutine reads in an EAM setfl file and populates the Towhee force field data structure.
ffrichar1995.F: this subroutine sets all of the parameters needed to build the Richards et al. 1995 force field.
ffshah2004.F: this subroutine sets all of the parameters needed to build the Shah and Maginn 2004 force field.
ffshukla1987.F: this subroutine sets all of the parameters needed to build the Shukla 1987 force field.
ffsks.F: this subroutine sets all of the parameters needed to build the SKS force field.
ffsmith1994.F: this subroutine sets all of the parameters needed to build the Smith and Dang 1994 force field.
ffsmmkmain.F: this subroutine sets all of the parameters needed to build the SMMK main force field.
ffsmmknaip.F: this subroutine sets all of the parameters needed to build the SMMK Note Added in Proof force field.
ffspce.F: this subroutine sets all of the parameters needed to build the SPC-E force field.
ffsquarewell.F: this subroutine sets all of the parameters needed to build the SquareWell force field.
ffstil1985.F: this subroutine sets all of the parameters needed to build the Stil1985 force field.
ffsum2003.F: this subroutine sets all of the parameters needed to build the Sum2003 force field.
fftele1987.F: this subroutine sets all of the parameters needed to build the Tele1987 force field.
fftip3p.F: this subroutine sets all of the parameters needed to build the TIP3P force field.
fftip4p.F: this subroutine sets all of the parameters needed to build the TIP4P force field.
fftip5p.F: this subroutine sets all of the parameters needed to build the TIP5P force field.
fftrappeeh.F: this subroutine sets all of the parameters needed to build the TraPPE-EH force field.
fftrappeua.F: this subroutine sets all of the parameters needed to build the TraPPE-UA force field.
fftrappeuaf.F: this subroutine sets all of the parameters needed to build the TraPPE-UA flexible force field.
ffuff.F: this subroutine sets all of the parameters needed to build the UFF force field.
ffunlu2004.F: this subroutine contains a partial implementation of the Unlu and Elliott 2004 force field.
ffvahid.F: a partial implementation of the SPEAD model of Vahid and Elliot.
ffvega1992.F: this subroutine sets all of the parameters needed to build the Vega et al. 1992 force field.
ffvink2001.F: this subroutine sets all of the parameters needed to build the Vink2001 force field.
ffwalt2001.F: this subroutine sets all of the parameters needed to build the Walt2001 force field.
ffweiner1984.F: this subroutine sets all of the parameters needed to build the Weiner et al. 1984 force field.
ffweiner1986.F: this subroutine sets all of the parameters needed to build the Weiner et al. 1986 force field.
ffwielop1985.F: this subroutine sets all of the parameters needed to build the Wielopolski and Smith 1985 force field.

The .c files

C routines

towhee.c: 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 mainloop.F.
control.c: 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.
jobfarm.c: 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.
rex.c: Implementation of Replica Exchange functionality. Replica Exchange requires MPI to run. While functional, it is currently at an early stage of development.
sturm.c: These routines handle much of the mathematics required for the concerted rotation moves.

Bug Reports

Towhee Bug Tracker

towhee-bugs@lists.sourceforge.net

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Last updated: July 22, 2021 Send comments to: Marcus Martin