From 0f69054d680af9931dba76a1f535e62ef37bb6db Mon Sep 17 00:00:00 2001 From: rjones Date: Wed, 21 Aug 2013 23:06:04 +0000 Subject: [PATCH] ATC version 2.0, date: Aug21 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10637 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-ATC/fix_atc.cpp | 55 +++++++++++++++++++++++++--------------- src/USER-ATC/fix_atc.h | 4 --- 2 files changed, 34 insertions(+), 25 deletions(-) diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index a4ddbebb73..66a21dacbe 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -41,6 +41,7 @@ using namespace LAMMPS_NS; using namespace FixConst; +using std::string; // main page of doxygen documentation /*! \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. \n For detailed exposition of the theory and algorithms please see:\n - - Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. An + - Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, An atomistic-to-continuum coupling method for heat transfer in solids. Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. \n - 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), A material frame approach for evaluating continuum variables in atomistic simulations. Journal of Computational Physics (2010), 229:2364. \n + - Templeton, JA; Jones, RE; Wagner, GJ, Application of a field-based method + to spatially varying thermal transport problems in molecular dynamics. + Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. \n + - Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, + Electron transport enhanced molecular dynamics for metals and semi-metals. + International Journal for Numerical Methods in Engineering (2010), 83:940. \n + - Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, + A long-range electric field solver for molecular dynamics based on + atomistic-to-continuum modeling. + Journal of Chemical Theory and Computation (2011), 7:1736. \n + - Mandadapu, KK; Templeton, JA; Lee, JW, Polarization as a field variable + from molecular dynamics simulations. + Journal of Chemical Physics (2013), 139:054115. \n Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element @@ -294,7 +308,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), } else { 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, array_atom, this, matParamFile); @@ -314,7 +328,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), } else { 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, array_atom, this, matParamFile); @@ -323,7 +337,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), // PhysicsTypes 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingEnergy(groupName, 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) { - std::string matParamFile = arg[4]; + string matParamFile = arg[4]; if (me==0) printf("ATC: constructing elastic coupling with parameter file %s\n",arg[4]); atc_ = new ATC::ATC_CouplingMomentum(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMomentum(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMomentum(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMomentum(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMomentum(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMass(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMass(groupName, 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) { - 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]); atc_ = new ATC::ATC_CouplingMomentumEnergy(groupName, array_atom, this, @@ -796,7 +810,6 @@ void FixATC::initial_integrate(int vflag) throw; } } - /* ---------------------------------------------------------------------- */ void FixATC::final_integrate() diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index ee383d76bd..11c5b909e7 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -10,9 +10,6 @@ FixStyle(atc,FixATC) #include "fix.h" #include "pointers.h" // access to lammps pointers -#include -using std::string; - namespace ATC { class ATC_Method; } @@ -41,7 +38,6 @@ namespace LAMMPS_NS { /** initial_integrate */ void initial_integrate(int vflag); - /** final_integrate */ void final_integrate();