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fix_rx.h
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rLAMMPS lammps
fix_rx.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle
(
rx
,
FixRX
)
#else
#ifndef LMP_FIX_RX_H
#define LMP_FIX_RX_H
#include "fix.h"
typedef
int
(
*
fnptr
)(
double
,
const
double
*
,
double
*
,
void
*
);
namespace
LAMMPS_NS
{
enum
{
ODE_LAMMPS_RK4
,
ODE_LAMMPS_RKF45
};
class
FixRX
:
public
Fix
{
public:
FixRX
(
class
LAMMPS
*
,
int
,
char
**
);
~
FixRX
();
int
setmask
();
void
post_constructor
();
virtual
void
init
();
void
init_list
(
int
,
class
NeighList
*
);
virtual
void
setup_pre_force
(
int
);
virtual
void
pre_force
(
int
);
protected:
int
pack_reverse_comm
(
int
,
int
,
double
*
);
void
unpack_reverse_comm
(
int
,
int
*
,
double
*
);
int
pack_forward_comm
(
int
,
int
*
,
double
*
,
int
,
int
*
);
void
unpack_forward_comm
(
int
,
int
,
double
*
);
class
NeighList
*
list
;
double
tmpArg
;
int
*
mol2param
;
// mapping from molecule to parameters
int
nreactions
;
// # of stored parameter sets
int
maxparam
;
// max # of parameter sets
struct
Param
{
double
cp
;
int
ispecies
;
char
*
name
;
// names of unique molecules and interaction type
};
Param
*
params
;
// parameter set for an I-J-K interaction
int
nspecies
;
void
read_file
(
char
*
);
void
setupParams
();
double
*
Arr
,
*
nArr
,
*
Ea
,
*
tempExp
;
double
**
stoich
,
**
stoichReactants
,
**
stoichProducts
;
double
*
kR
;
//!< Classic Runge-Kutta 4th-order stepper.
void
rk4
(
int
,
double
*
,
void
*
);
//!< Runge-Kutta-Fehlberg ODE Solver.
void
rkf45
(
int
,
double
*
,
void
*
,
int
ode_counter
[]);
//!< Runge-Kutta-Fehlberg ODE stepper function.
void
rkf45_step
(
const
int
neq
,
const
double
h
,
double
y
[],
double
y_out
[],
double
rwk
[],
void
*
);
//!< Initial step size estimation for the Runge-Kutta-Fehlberg ODE solver.
int
rkf45_h0
(
const
int
neq
,
const
double
t
,
const
double
t_stop
,
const
double
hmin
,
const
double
hmax
,
double
&
h0
,
double
y
[],
double
rwk
[],
void
*
v_params
);
class
PairDPDfdtEnergy
*
pairDPDE
;
double
*
dpdThetaLocal
;
double
*
sumWeights
;
void
computeLocalTemperature
();
int
localTempFlag
,
wtFlag
,
odeIntegrationFlag
;
double
sigFactor
;
int
rhs
(
double
,
const
double
*
,
double
*
,
void
*
);
int
rhs_dense
(
double
,
const
double
*
,
double
*
,
void
*
);
// User-defined data container needed in rhs.
struct
UserRHSData
{
double
*
kFor
;
double
*
rxnRateLaw
;
};
// Sparse stoichiometric matrix storage format and methods.
bool
useSparseKinetics
;
//SparseKinetics sparseKinetics;
void
initSparse
(
void
);
int
rhs_sparse
(
double
,
const
double
*
,
double
*
,
void
*
)
const
;
int
sparseKinetics_maxReactants
;
//<! Max # of reactants species in any reaction
int
sparseKinetics_maxProducts
;
//<! Max # of product species in any reaction
int
sparseKinetics_maxSpecies
;
//<! Max # of species (maxReactants + maxProducts) in any reaction
//! Objects to hold the stoichiometric coefficients using a sparse matrix
//! format. Enables a sparse formulation for the reaction rates:
//! \f${\omega}_i = \Pi_{j=1}^{NS_i} K^{f}_i [x_j]^{\nu^{'}_{ij}} -
//! K^{r}_i x_j^{\nu^{''}_{ij}}\f$.
double
**
sparseKinetics_nu
;
//<! Stoichiometric matrix with FLT values.
int
**
sparseKinetics_nuk
;
//<! Index (base-0) of species ... this is the column sparse matrix.
int
**
sparseKinetics_inu
;
//<! Stoichiometric matrix with integral values.
bool
*
sparseKinetics_isIntegralReaction
;
//<! Flag indicating if a reaction has integer stoichiometric values.
// ODE Parameters
int
minSteps
;
//!< Minimum # of steps for the ODE solver(s).
int
maxIters
;
//!< Maximum # of iterations for the ODE solver(s).
double
relTol
,
absTol
;
//!< Relative and absolute tolerances for the ODE solver(s).
// ODE Diagnostics
//int nSteps; //!< # of accepted steps taken over all atoms.
//int nIters; //!< # of attemped steps for all atoms.
//int nFuncs; //!< # of RHS evaluations for all atoms.
//int nFails; //!< # of ODE systems that failed (for some reason).
int
diagnosticFrequency
;
//!< Frequency (LMP steps) that run-time diagnostics will be printed to the log.
enum
{
numDiagnosticCounters
=
5
};
enum
{
StepSum
=
0
,
FuncSum
,
TimeSum
,
AtomSum
,
CountSum
};
double
diagnosticCounter
[
numDiagnosticCounters
];
int
*
diagnosticCounterPerODE
[
numDiagnosticCounters
];
//!< ODE Solver diagnostics.
void
odeDiagnostics
(
void
);
private:
char
*
kineticsFile
;
char
*
id_fix_species
,
*
id_fix_species_old
;
class
FixPropertyAtom
*
fix_species
,
*
fix_species_old
;
int
restartFlag
;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: fix rx cannot be combined with fix property/atom
Self-explanatory
E: Cannot open rx file %s
Self-explanatory
E: Exceeded the maximum number of species permitted in fix rx
Reduce the number of species in the fix rx reaction kinetics file
E: There are no rx species specified.
Self-explanatory
E: Must use pair_style dpd/fdt/energy with fix rx.
Self-explanatory
E: fix rx requires fix eos/table/rx to be specified.
Self-explanatory
W: in FixRX::pre_force, ODE solver failed for %d atoms.
Self-explanatory
E: Missing parameters in reaction kinetic equation.
Self-explanatory
E: Potential file has duplicate entry.
Self-explanatory
E: Computed concentration in RK4 (RKF45) solver is < -1.0e-10.
Self-explanatory: Adjust settings for the RK4 solver.
*/
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