forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15355 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
87bfe1941b
commit
cff65b956a
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@ -687,7 +687,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
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// Store the current thetai in t1
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t1 = MAX(thetai,tb->lo);
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t1 = MIN(thetai,tb->hi);
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t1 = MIN(t1,tb->hi);
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if(t1==tb->hi) delta = -delta;
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// Compute u1 at thetai
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@ -388,7 +388,7 @@ void FixRX::post_constructor()
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/* ---------------------------------------------------------------------- */
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int FixRX::initSparse()
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void FixRX::initSparse()
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{
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const int Verbosity = 1;
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@ -637,9 +637,8 @@ void FixRX::setup_pre_force(int vflag)
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int nlocal = atom->nlocal;
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int nghost = atom->nghost;
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int *mask = atom->mask;
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double *dpdTheta = atom->dpdTheta;
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int newton_pair = force->newton_pair;
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double tmp, theta;
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double tmp;
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int ii;
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if(localTempFlag){
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@ -662,8 +661,6 @@ void FixRX::setup_pre_force(int vflag)
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}
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit){
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if(localTempFlag) theta = dpdThetaLocal[i];
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else theta=dpdTheta[i];
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// Set the reaction rate constants to zero: no reactions occur at step 0
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for(int irxn=0;irxn<nreactions;irxn++)
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@ -692,8 +689,6 @@ void FixRX::pre_force(int vflag)
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int ii;
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double theta;
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TimerType timer_start = getTimeStamp();
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if(localTempFlag){
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if (newton_pair) {
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dpdThetaLocal = new double[nlocal+nghost];
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@ -705,7 +700,6 @@ void FixRX::pre_force(int vflag)
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dpdThetaLocal[ii] = 0.0;
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}
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computeLocalTemperature();
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double *dpdTheta = this->dpdThetaLocal;
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}
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TimerType timer_localTemperature = getTimeStamp();
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@ -746,14 +740,7 @@ void FixRX::pre_force(int vflag)
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comm->forward_comm_fix(this);
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if(localTempFlag) delete [] dpdThetaLocal;
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TimerType timer_stop = getTimeStamp();
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double time_ODE = getElapsedTime(timer_localTemperature, timer_ODE);
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// printf("FixRX::pre_force total= %e Temp= %e ODE= %e Comm= %e nlocal= %d %d %d %d %d\n",
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// getElapsedTime(timer_start, timer_stop),
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// (localTempFlag) ? getElapsedTime(timer_start, timer_localTemperature) : 0.0,
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// time_ODE,
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// getElapsedTime(timer_ODE, timer_stop),
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// nlocal, nSteps, nIters, nFuncs, nFails);
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// Warn the user if a failure was detected in the ODE solver.
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if (nFails > 0){
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@ -904,6 +891,7 @@ void FixRX::read_file(char *file)
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error->all(FLERR,"Illegal fix rx command");
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}
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word = strtok(NULL, " \t\n\r\f");
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if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation");
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if(strcmp(word,"=") == 0) sign = 1.0;
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if(strcmp(word,"+") != 0 && strcmp(word,"=") != 0){
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if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation");
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@ -1034,12 +1022,9 @@ void FixRX::rk4(int id, double *rwork)
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void FixRX::rkf45_step (const int neq, const double h, double y[], double y_out[], double rwk[], void* v_param)
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{
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const double c20=0.25;
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const double c21=0.25;
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const double c30=0.375;
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const double c31=0.09375;
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const double c32=0.28125;
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const double c40=0.92307692307692;
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const double c41=0.87938097405553;
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const double c42=-3.2771961766045;
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const double c43=3.3208921256258;
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@ -1047,19 +1032,16 @@ void FixRX::rkf45_step (const int neq, const double h, double y[], double y_out[
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const double c52=-8.0;
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const double c53=7.1734892787524;
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const double c54=-0.20589668615984;
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const double c60=0.5;
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const double c61=-0.2962962962963;
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const double c62=2.0;
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const double c63=-1.3816764132554;
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const double c64=0.45297270955166;
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const double c65=-0.275;
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const double a1=0.11574074074074;
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const double a2=0.0;
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const double a3=0.54892787524366;
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const double a4=0.5353313840156;
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const double a5=-0.2;
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const double b1=0.11851851851852;
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const double b2=0.0;
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const double b3=0.51898635477583;
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const double b4=0.50613149034201;
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const double b5=-0.18;
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@ -1146,10 +1128,6 @@ int FixRX::rkf45_h0 (const int neq, const double t, const double t_stop,
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const double hmin, const double hmax,
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double& h0, double y[], double rwk[], void* v_params)
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{
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const double uround = DBL_EPSILON;
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const double tdist = fabs(t_stop - t);
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const double tround = tdist * uround;
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// Set lower and upper bounds on h0, and take geometric mean as first trial value.
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// Exit with this value if the bounds cross each other.
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@ -1696,7 +1674,7 @@ void FixRX::computeLocalTemperature()
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int newton_pair = force->newton_pair;
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// local temperature variables
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double wij=0.0, fr, fr4;
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double wij=0.0;
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double *dpdTheta = atom->dpdTheta;
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// Initialize the local density and local temperature arrays
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@ -1738,8 +1716,6 @@ void FixRX::computeLocalTemperature()
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if (rsq < pairDPDE->cutsq[itype][jtype]) {
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double rcut = sqrt(pairDPDE->cutsq[itype][jtype]);
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double rij = sqrt(rsq);
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double tmpFactor = 1.0-rij/rcut;
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double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
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double ratio = rij/rcut;
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// Lucy's Weight Function
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@ -90,7 +90,7 @@ class FixRX : public Fix {
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// Sparse stoichiometric matrix storage format and methods.
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bool useSparseKinetics;
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//SparseKinetics sparseKinetics;
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int initSparse(void);
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void initSparse(void);
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int rhs_sparse(double, const double *, double *, void *) const;
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int sparseKinetics_maxReactants; //<! Max # of reactants species in any reaction
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@ -93,7 +93,7 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype,itable;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair;
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double rsq,factor_lj;
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double rsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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Table *tb;
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@ -109,13 +109,11 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nghost = atom->nghost;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double fractionOld1_i,fractionOld1_j;
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double fractionOld2_i,fractionOld2_j;
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double fraction1_i,fraction1_j;
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double fraction2_i,fraction2_j;
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double fraction1_i;
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double *uCG = atom->uCG;
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double *uCGnew = atom->uCGnew;
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@ -166,11 +164,9 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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fractionOld1_i = fractionOld1[i];
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fractionOld2_i = fractionOld2[i];
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fraction1_i = fraction1[i];
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fraction2_i = fraction2[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_lj = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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@ -184,8 +180,6 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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fractionOld1_j = fractionOld1[j];
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fractionOld2_j = fractionOld2[j];
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fraction1_j = fraction1[j];
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fraction2_j = fraction2[j];
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tb = &tables[tabindex[itype][jtype]];
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if (rho[i]*rho[i] < tb->innersq || rho[j]*rho[j] < tb->innersq){
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@ -205,8 +199,10 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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}
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A_i = tb->f[itable];
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A_j = tb->f[jtable];
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fpair = 0.5*(A_i + A_j)*(1.0+3.0*sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]));
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fpair = fpair/sqrt(rsq);
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const double rfactor = 1.0-sqrt(rsq/cutsq[itype][jtype]);
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fpair = 0.5*(A_i + A_j)*(4.0-3.0*rfactor)*rfactor*rfactor*rfactor;
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fpair /= sqrt(rsq);
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} else if (tabstyle == LINEAR) {
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itable = static_cast<int> ((rho[i]*rho[i] - tb->innersq) * tb->invdelta);
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@ -232,9 +228,9 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
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A_i = tb->f[itable] + fraction_i*tb->df[itable];
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A_j = tb->f[jtable] + fraction_j*tb->df[jtable];
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fpair = 0.5*(A_i + A_j)*(1.0+3.0*sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(1.0 - sqrt(rsq)/sqrt(cutsq[itype][jtype]));
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fpair = fpair / sqrt(rsq);
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const double rfactor = 1.0-sqrt(rsq/cutsq[itype][jtype]);
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fpair = 0.5*(A_i + A_j)*(4.0-3.0*rfactor)*rfactor*rfactor*rfactor;
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fpair /= sqrt(rsq);
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} else error->one(FLERR,"Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx");
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@ -389,15 +385,11 @@ void PairMultiLucyRX::coeff(int narg, char **arg)
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// insure cutoff is within table
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if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length");
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double rlo,rhi;
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if (tb->rflag == 0) {
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rlo = tb->rfile[0];
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rhi = tb->rfile[tb->ninput-1];
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rho_0 = tb->rfile[0];
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} else {
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rlo = tb->rlo;
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rhi = tb->rhi;
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rho_0 = tb->rlo;
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}
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rho_0 = rlo;
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tb->match = 0;
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if (tabstyle == LINEAR && tb->ninput == tablength &&
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@ -903,8 +895,8 @@ void PairMultiLucyRX::computeLocalDensity()
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const double delz = ztmp - x[j][2];
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const double rsq = delx*delx + dely*dely + delz*delz;
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if (one_type)
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if (rsq < cutsq_type11){
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if (one_type) {
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if (rsq < cutsq_type11) {
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const double rcut = rcut_type11;
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const double r_over_rcut = sqrt(rsq) / rcut;
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const double tmpFactor = 1.0 - r_over_rcut;
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@ -913,9 +905,7 @@ void PairMultiLucyRX::computeLocalDensity()
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rho_i += factor;
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if (newton_pair || j < nlocal)
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rho[j] += factor;
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}
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else
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if (rsq < cutsq[itype][jtype]){
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} else if (rsq < cutsq[itype][jtype]) {
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const double rcut = sqrt(cutsq[itype][jtype]);
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const double tmpFactor = 1.0-sqrt(rsq)/rcut;
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const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
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@ -924,6 +914,7 @@ void PairMultiLucyRX::computeLocalDensity()
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if (newton_pair || j < nlocal)
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rho[j] += factor;
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}
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}
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}
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rho[i] = rho_i;
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@ -1036,7 +1036,7 @@ void DumpImage::create_image()
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// render objects provided by a fix
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if (fixflag) {
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int tridraw,edgedraw;
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int tridraw=0,edgedraw=0;
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if (domain->dimension == 3) {
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tridraw = 1;
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edgedraw = 1;
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