lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

ATC version 2.0, date: Aug21 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10637 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones 2013-08-21 23:06:04 +00:00
parent 7d0fe14fdb
commit 0f69054d68
2 changed files with 34 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

55
src/USER-ATC/fix_atc.cpp
View File

@ -41,6 +41,7 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
using std::string;
// main page of doxygen documentation // main page of doxygen documentation
/*! \mainpage AtC : Atom-to-Continuum methods /*! \mainpage AtC : Atom-to-Continuum methods
@ -148,7 +149,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
using separate fixes. using separate fixes.
\n \n
For detailed exposition of the theory and algorithms please see:\n For detailed exposition of the theory and algorithms please see:\n
- Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. <VAR> An - Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <VAR> An
atomistic-to-continuum coupling method for heat transfer in solids. </VAR> atomistic-to-continuum coupling method for heat transfer in solids. </VAR>
Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. \n Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. \n
- Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, - Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ,
@ -159,6 +160,19 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
<VAR> A material frame approach for evaluating continuum variables in <VAR> A material frame approach for evaluating continuum variables in
atomistic simulations. </VAR> atomistic simulations. </VAR>
Journal of Computational Physics (2010), 229:2364. \n Journal of Computational Physics (2010), 229:2364. \n
- Templeton, JA; Jones, RE; Wagner, GJ, <VAR> Application of a field-based method
to spatially varying thermal transport problems in molecular dynamics. </VAR>
Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. \n
- Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <VAR>
Electron transport enhanced molecular dynamics for metals and semi-metals. </VAR>
International Journal for Numerical Methods in Engineering (2010), 83:940. \n
- Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM,
<VAR> A long-range electric field solver for molecular dynamics based on
atomistic-to-continuum modeling. </VAR>
Journal of Chemical Theory and Computation (2011), 7:1736. \n
- Mandadapu, KK; Templeton, JA; Lee, JW, <VAR> Polarization as a field variable
from molecular dynamics simulations. </VAR>
Journal of Chemical Physics (2013), 139:054115. \n
Please refer to the standard Please refer to the standard
finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
@ -294,7 +308,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else { else {
if (me==0) printf("ATC: constructing shape function field estimate with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing shape function field estimate with parameter file %s\n",arg[4]);
std::string matParamFile = arg[4]; string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName, atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName,
array_atom, this, array_atom, this,
matParamFile); matParamFile);
@ -314,7 +328,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else { else {
if (me==0) printf("ATC: constructing kernel field estimate with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing kernel field estimate with parameter file %s\n",arg[4]);
std::string matParamFile = arg[4]; string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferKernel(groupName, atc_ = new ATC::ATC_TransferKernel(groupName,
array_atom, this, array_atom, this,
matParamFile); matParamFile);
@ -323,7 +337,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
// PhysicsTypes // PhysicsTypes
else if (strcmp(arg[3],"thermal")==0) else if (strcmp(arg[3],"thermal")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermal coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing thermal coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -331,7 +345,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"two_temperature")==0) else if (strcmp(arg[3],"two_temperature")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing two_temperature coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing two_temperature coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -339,7 +353,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"drift_diffusion")==0) else if (strcmp(arg[3],"drift_diffusion")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing drift_diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -347,7 +361,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"drift_diffusion-equilibrium")==0) else if (strcmp(arg[3],"drift_diffusion-equilibrium")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -355,7 +369,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"drift_diffusion-schrodinger")==0) else if (strcmp(arg[3],"drift_diffusion-schrodinger")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -363,7 +377,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"drift_diffusion-schrodinger-slice")==0) else if (strcmp(arg[3],"drift_diffusion-schrodinger-slice")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file %s\n",arg[4]); if (me==0) printf("Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -371,7 +385,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"convective_drift_diffusion")==0) else if (strcmp(arg[3],"convective_drift_diffusion")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing convective_drift_diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -379,7 +393,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"convective_drift_diffusion-equilibrium")==0) else if (strcmp(arg[3],"convective_drift_diffusion-equilibrium")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing convective_drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -387,7 +401,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"convective_drift_diffusion-schrodinger")==0) else if (strcmp(arg[3],"convective_drift_diffusion-schrodinger")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingEnergy(groupName, atc_ = new ATC::ATC_CouplingEnergy(groupName,
array_atom, this, array_atom, this,
@ -395,7 +409,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"elastic")==0) else if (strcmp(arg[3],"elastic")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing elastic coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing elastic coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName, atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this, array_atom, this,
@ -404,7 +418,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"electrostatic")==0) else if (strcmp(arg[3],"electrostatic")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing electrostatic mechanical coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing electrostatic mechanical coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName, atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this, array_atom, this,
@ -414,7 +428,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"electrostatic-equilibrium")==0) else if (strcmp(arg[3],"electrostatic-equilibrium")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing equilibrium electrostatic coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing equilibrium electrostatic coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName, atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this, array_atom, this,
@ -424,7 +438,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"shear")==0) else if (strcmp(arg[3],"shear")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing viscous/shear coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing viscous/shear coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName, atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this, array_atom, this,
@ -433,7 +447,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"electrostatic_equilibrium")==0) else if (strcmp(arg[3],"electrostatic_equilibrium")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (electrostatic_equilibrium) with parameter file %s\n",arg[4]); if (me==0) printf("Constructing ATC transfer (electrostatic_equilibrium) with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentum(groupName, atc_ = new ATC::ATC_CouplingMomentum(groupName,
array_atom, this, array_atom, this,
@ -443,7 +457,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"species")==0) else if (strcmp(arg[3],"species")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing species diffusion coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing species diffusion coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMass(groupName, atc_ = new ATC::ATC_CouplingMass(groupName,
array_atom, this, array_atom, this,
@ -451,7 +465,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"species_electrostatic")==0) else if (strcmp(arg[3],"species_electrostatic")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing electrostatic species coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing electrostatic species coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMass(groupName, atc_ = new ATC::ATC_CouplingMass(groupName,
array_atom, this, array_atom, this,
@ -459,7 +473,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
} }
else if (strcmp(arg[3],"thermo_elastic")==0) else if (strcmp(arg[3],"thermo_elastic")==0)
{ {
std::string matParamFile = arg[4]; string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermo-mechanical coupling with parameter file %s\n",arg[4]); if (me==0) printf("ATC: constructing thermo-mechanical coupling with parameter file %s\n",arg[4]);
atc_ = new ATC::ATC_CouplingMomentumEnergy(groupName, atc_ = new ATC::ATC_CouplingMomentumEnergy(groupName,
array_atom, this, array_atom, this,
@ -796,7 +810,6 @@ void FixATC::initial_integrate(int vflag)
throw; throw;
} }
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixATC::final_integrate() void FixATC::final_integrate()

4
src/USER-ATC/fix_atc.h
View File

@ -10,9 +10,6 @@ FixStyle(atc,FixATC)
#include "fix.h" #include "fix.h"
#include "pointers.h" // access to lammps pointers #include "pointers.h" // access to lammps pointers
#include <string>
using std::string;
namespace ATC { namespace ATC {
class ATC_Method; class ATC_Method;
} }
@ -41,7 +38,6 @@ namespace LAMMPS_NS {
/** initial_integrate */ /** initial_integrate */
void initial_integrate(int vflag); void initial_integrate(int vflag);
/** final_integrate */ /** final_integrate */
void final_integrate(); void final_integrate();