dpsim - Simulate water with induced dipoles solved self-consistently.
  Domain is periodic cube (determined by nmolPerLine, below).
  Dynamical integration methods include constant energy and constant
  temperature.  Provides long-range electrostatics with modified PME
  for dipolar interactions.

syntax:  dpsim 'configfile'

where 'configfile' has similar syntax with mdsim config files, i.e.,
parameters set by 'option [=] value', capitalization is irrelevant,
and '#' denotes comment to end-of-line.

The list of parameters and their values follows.

parameter       value
---------       -----

mdtype          constEnergy - simulate using micro-canonical ensemble
                NoseHoover  - canonical ensemble with Nose-Hoover thermostat
                Berendsen   - canonical ensemble with Berendsen thermostat

model           RPOL  - revised POL water model (polar, rigid)
                POL1  - POL1 water model (polar, rigid)
                POL3  - POL3 water model (polar, rigid)
                SPC   - SPC water model (non-polar, rigid)
                ARGON - argon simulation, for testing

elecSolver      PME   - smooth PME (using cubic B-spline interpolation)
                Ewald - standard Ewald, for testing
                (defaults to cutoff simulation unless specified)

nThernalSteps   'INTEGER' - number of steps for thermalization

nSteps          'INTEGER' - number of steps for production run

dipoleSolver    Picard
                dampedPicard
                CG
                JCG_X
                JCG_R
                QCG_X
                PCG_X
                PCG_R
                MCG_X
                Chebyshev
                - these are compared in Wei Wang's dissertation,
                  defaults to MCG_X ("peek" CG)

predictType     polynomial
                diffPolynomial
                timeReversible
                timeReversible_HighOrder
                zero
                leastSquares
                constrainLeastSquares
                diffLeastSquares
                timeReversibleLeastSquares
                - these are compared in Wei Wang's dissertation,
                  defaults to leastSquare

predictDegree   - degree of prediction polynomial, defaults to 6

maxIterations   - max iterations for self-consistency, defaults to 10

errorTolerance  - error tolerance for convergence, defaults to 1e-12

nmolPerLine     - The number of molecules per line (i.e. side of cube),
                  a required parameter.  The program begins with water
                  molecules placed on a lattice with size indicated by
                  this parameter, and the dimension of the periodic box
                  is determined from this.  Restarted simulations also
                  require this parameter to determine the expected number
                  of water molecules to read.

fromRestartFile 'FILENAME' - give full name of pos and vel restart

temperature     'DOUBLE' - initial temperature, defaults to 300 K for water

cutoff          'DOUBLE' - cutoff distance, defaults to 8 A for *POL* models

switchdist      'DOUBLE' - for van der Waals, defaults to 6 A for *POL* models

timestep        'DOUBLE' - defaults to 1 femtosecond for water

dielectric      'DOUBLE' - defaults to 1.0

scaling14       'DOUBLE' - defaults to 1.0

exclude         none / 1-2 / 1-3 / 1-4 / scaled1-4 - defaults to 1-3

outputEnergies  'INTEGER' - number of steps between energy output,
                            defaults to 10

firsttimestep   'INTEGER' - first time step number, defaults to 0

restartfreq     'INTEGER' - number of steps between restart file output,
                            defaults to 1000

restartsave     on / off - retain all restart files? defaults to off (no)

restartname     'BASE FILENAME' - _%d.dat is appended, where %d is step
                  number, defaults to pos_vel

forcedumpname   'BASE FILENAME' - _%d.dat is appended, where %d is step
                  number, defaults to dipoles

dcdfreq         'INTEGER' - number of steps between DCD frames

dcdfile         'BASE FILENAME' - generates both .pdb and .dcd for
                  production run using same base filename

dcdthermalfile  'BASE FILENAME' - generates both .pdb and .dcd for
                  thermalization using same base filename

-------------------------------------------------------------------------------

# example dpsim config file for constant energy

mdtype          ConstEnergy
model           Rpol
elecSolver      pme

nmolperline     6
timestep        2.0
nthermalsteps   200
nsteps          500
restartfreq     100
restartsave     on

outputEnergies  10

dcdfreq         50
dcdthermalfile  thermal
dcdfile         prodrun

-------------------------------------------------------------------------------

# example dpsim config file for Nose-Hoover

mdtype          NoseHoover
model           Rpol
elecSolver      pme

predictType     Polynomial
predictDegree   4

nmolperline     6
timestep        1.0
nthermalsteps   400
nsteps          1000
restartfreq     200
restartsave     on
restartname     nh_pos_vel
forcedumpname   nh_dipoles

outputEnergies  20

dcdfreq         100
dcdthermalfile  nh_thermal
dcdfile         nh_prodrun
