From 0e6bbf8dffed7483bca320d66cc0347070dc0c48 Mon Sep 17 00:00:00 2001 From: rohskopf Date: Fri, 17 Jun 2022 14:16:03 -0600 Subject: [PATCH] Remove files from other branch. --- src/fix_move.cpp | 247 ++--------------------------------------------- src/fix_move.h | 55 ----------- 2 files changed, 8 insertions(+), 294 deletions(-) diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 7cf5567028..37e8647671 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -35,16 +35,11 @@ #include #include -#include -#include -#include -#include - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum { LINEAR, WIGGLE, ROTATE, VARIABLE, TRANSROT, WIGGLE_EIGEN }; +enum { LINEAR, WIGGLE, ROTATE, VARIABLE, TRANSROT }; enum { EQUAL, ATOM }; #define INERTIA 0.2 // moment of inertia prefactor for ellipsoid @@ -192,80 +187,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR, "Illegal fix move command"); - } - // Fix move wiggle_eigen - else if (strcmp(arg[3], "wiggle_eigen") == 0) { - int natoms = atom->natoms; - int nlocal = atom->nlocal; - printf("----- fix move wiggle_eigen initialize -----\n"); - printf("natoms: %d\n", natoms); - memory->create(emat,natoms*3,natoms*3,"move:emat"); - memory->create(freq,natoms*3,"move:freq"); - - // Read EMAT - std::ifstream readfile2; - for (int i = 0; i < natoms*3; i++) { - for (int j = 0; j < natoms*3; j++) { - emat[i][j] = 0.0; - } - } - readfile2.open("../EMAT"); - //readfile2.open("ev_real.txt"); - if (!readfile2.is_open()) { - //printf("ASDFASDF"); - printf("Unable to open ../EMAT\n"); - exit(1); - } - //printf("natoms: %d\n", natoms); - for (int i=0;i<3*natoms;i++){ - for (int j=0;j<3*natoms;j++){ - readfile2>>emat[i][j]; - } - } - - // Read FREQUENCIES - std::ifstream readfile3; - for (int i = 0; i < natoms*3; i++) { - freq[i]=0.0; - } - readfile3.open("FREQUENCIES"); - //readfile2.open("ev_real.txt"); - - if (!readfile3.is_open()) { - printf("Unable to open FREQUENCIES.\n"); - exit(1); - } - //printf("natoms: %d\n", natoms); - for (int i=0;i<3*natoms;i++){ - readfile3>>freq[i]; - } - - - if (narg < 8) error->all(FLERR, "Illegal fix move command"); - iarg = 8; - mstyle = WIGGLE_EIGEN; - if (strcmp(arg[4], "NULL") == 0) - axflag = 0; - else { - axflag = 1; - ax = utils::numeric(FLERR, arg[4], false, lmp); - } - if (strcmp(arg[5], "NULL") == 0) - ayflag = 0; - else { - ayflag = 1; - ay = utils::numeric(FLERR, arg[5], false, lmp); - } - if (strcmp(arg[6], "NULL") == 0) - azflag = 0; - else { - azflag = 1; - az = utils::numeric(FLERR, arg[6], false, lmp); - } - period = utils::numeric(FLERR, arg[7], false, lmp); - if (period <= 0.0) error->all(FLERR, "Illegal fix move command"); - } - else + } else error->all(FLERR, "Illegal fix move command"); // optional args @@ -314,10 +236,6 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : if (axflag) ax *= xscale; if (ayflag) ay *= yscale; if (azflag) az *= zscale; - } else if (mstyle == WIGGLE_EIGEN) { - if (axflag) ax *= xscale; - if (ayflag) ay *= yscale; - if (azflag) az *= zscale; } else if (mstyle == ROTATE) { point[0] *= xscale; point[1] *= yscale; @@ -334,7 +252,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : // set omega_rotate from period - if ((mstyle == WIGGLE) || (mstyle == ROTATE) || (mstyle == TRANSROT) || (mstyle == WIGGLE_EIGEN)) + if ((mstyle == WIGGLE) || (mstyle == ROTATE) || (mstyle == TRANSROT)) omega_rotate = MY_2PI / period; // runit = unit vector along rotation axis @@ -377,10 +295,10 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : // AtomVec pointers to retrieve per-atom storage of extra quantities - avec_ellipsoid = dynamic_cast( atom->style_match("ellipsoid")); - avec_line = dynamic_cast( atom->style_match("line")); - avec_tri = dynamic_cast( atom->style_match("tri")); - avec_body = dynamic_cast( atom->style_match("body")); + avec_ellipsoid = dynamic_cast(atom->style_match("ellipsoid")); + avec_line = dynamic_cast(atom->style_match("line")); + avec_tri = dynamic_cast(atom->style_match("tri")); + avec_body = dynamic_cast(atom->style_match("body")); // xoriginal = initial unwrapped positions of atoms // toriginal = initial theta of lines @@ -462,11 +380,6 @@ FixMove::~FixMove() memory->destroy(displace); memory->destroy(velocity); - if (mstyle==WIGGLE_EIGEN){ - memory->destroy(emat); - memory->destroy(freq); - } - delete[] xvarstr; delete[] yvarstr; delete[] zvarstr; @@ -582,7 +495,7 @@ void FixMove::init() velocity = nullptr; if (utils::strmatch(update->integrate_style, "^respa")) - nlevels_respa = (dynamic_cast( update->integrate))->nlevels; + nlevels_respa = (dynamic_cast(update->integrate))->nlevels; } /* ---------------------------------------------------------------------- @@ -614,7 +527,6 @@ void FixMove::initial_integrate(int /*vflag*/) int *tri = atom->tri; int *body = atom->body; int *mask = atom->mask; - int *tag = atom->tag; int nlocal = atom->nlocal; @@ -740,142 +652,6 @@ void FixMove::initial_integrate(int /*vflag*/) // X = P + C + A cos(w*dt) + B sin(w*dt) // V = w R0 cross (A cos(w*dt) + B sin(w*dt)) -} else if (mstyle == WIGGLE_EIGEN) { - //printf("----- Wiggling!-----\n"); - int modeindx = 10; - //printf("%f %f\n", omega_rotate, MY_2PI*freq[modeindx]); - omega_rotate = MY_2PI*freq[modeindx]; - double arg = omega_rotate * delta; - double sine = sin(arg); - double cosine = cos(arg); - - //printf("arg: %f\n", arg); - for (int alpha=0; alpha<3; alpha++){ - for (int i=0; iremap_near(x[i], xold); - } - - } - - - } - - /* - for (int i=0; iremap_near(x[i], xold); - } - - } - */ - - /* - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { - xold[0] = x[i][0]; - xold[1] = x[i][1]; - xold[2] = x[i][2]; - - if (axflag) { - v[i][0] = ax * omega_rotate * cosine; - x[i][0] = xoriginal[i][0] + ax * sine; - } else if (rmass) { - dtfm = dtf / rmass[i]; - v[i][0] += dtfm * f[i][0]; - x[i][0] += dtv * v[i][0]; - } else { - dtfm = dtf / mass[type[i]]; - v[i][0] += dtfm * f[i][0]; - x[i][0] += dtv * v[i][0]; - } - - if (ayflag) { - v[i][1] = ay * omega_rotate * cosine; - x[i][1] = xoriginal[i][1] + ay * sine; - } else if (rmass) { - dtfm = dtf / rmass[i]; - v[i][1] += dtfm * f[i][1]; - x[i][1] += dtv * v[i][1]; - } else { - dtfm = dtf / mass[type[i]]; - v[i][1] += dtfm * f[i][1]; - x[i][1] += dtv * v[i][1]; - } - - if (azflag) { - v[i][2] = az * omega_rotate * cosine; - x[i][2] = xoriginal[i][2] + az * sine; - } else if (rmass) { - dtfm = dtf / rmass[i]; - v[i][2] += dtfm * f[i][2]; - x[i][2] += dtv * v[i][2]; - } else { - dtfm = dtf / mass[type[i]]; - v[i][2] += dtfm * f[i][2]; - x[i][2] += dtv * v[i][2]; - } - - domain->remap_near(x[i], xold); - } - } - */ - // for rotate by right-hand rule around omega: - // P = point = vector = point of rotation - // R = vector = axis of rotation - // w = omega of rotation (from period) - // X0 = xoriginal = initial coord of atom - // R0 = runit = unit vector for R - // D = X0 - P = vector from P to X0 - // C = (D dot R0) R0 = projection of atom coord onto R line - // A = D - C = vector from R line to X0 - // B = R0 cross A = vector perp to A in plane of rotation - // A,B define plane of circular rotation around R line - // X = P + C + A cos(w*dt) + B sin(w*dt) - // V = w R0 cross (A cos(w*dt) + B sin(w*dt)) - } else if (mstyle == ROTATE) { double arg = omega_rotate * delta; double cosine = cos(arg); @@ -1527,13 +1303,6 @@ void FixMove::set_arrays(int i) if (ayflag) xoriginal[i][1] -= ay * sine; if (azflag) xoriginal[i][2] -= az * sine; -} else if (mstyle == WIGGLE_EIGEN) { - double arg = omega_rotate * delta; - double sine = sin(arg); - if (axflag) xoriginal[i][0] -= ax * sine; - if (ayflag) xoriginal[i][1] -= ay * sine; - if (azflag) xoriginal[i][2] -= az * sine; - } else if (mstyle == ROTATE) { double a[3], b[3], c[3], d[3], disp[3], ddotr; double arg = -omega_rotate * delta; diff --git a/src/fix_move.h b/src/fix_move.h index 8023a66c1b..e6b253a2a2 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -73,11 +73,6 @@ class FixMove : public Fix { int maxatom; double **displace, **velocity; - // fix move wiggle_eigen variables - - double **emat; - double *freq; - class AtomVecEllipsoid *avec_ellipsoid; class AtomVecLine *avec_line; class AtomVecTri *avec_tri; @@ -88,53 +83,3 @@ class FixMove : public Fix { #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 move cannot set linear z motion for 2d problem - -Self-explanatory. - -E: Fix move cannot set wiggle z motion for 2d problem - -Self-explanatory. - -E: Fix move cannot rotate around non z-axis for 2d problem - -UNDOCUMENTED - -E: Fix move cannot define z or vz variable for 2d problem - -Self-explanatory. - -E: Zero length rotation vector with fix move - -Self-explanatory. - -E: Variable name for fix move does not exist - -Self-explanatory. - -E: Variable for fix move is invalid style - -Only equal-style variables can be used. - -E: Cannot add atoms to fix move variable - -Atoms can not be added afterwards to this fix option. - -E: Resetting timestep size is not allowed with fix move - -This is because fix move is moving atoms based on elapsed time. - -U: Fix move cannot rotate aroung non z-axis for 2d problem - -Self-explanatory. - -*/