refactor group access, enable and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -40,10 +39,10 @@ using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr),
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estr(nullptr), idregion(nullptr), efield(nullptr)
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Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
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idregion(nullptr), region(nullptr), efield(nullptr)
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{
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if (narg < 6) error->all(FLERR,"Illegal fix efield command");
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if (narg < 6) error->all(FLERR, "Illegal fix efield command");
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dynamic_group_allow = 1;
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vector_flag = 1;
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@ -60,56 +59,53 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
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qe2f = force->qe2f;
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xstr = ystr = zstr = nullptr;
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if (utils::strmatch(arg[3],"^v_")) {
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xstr = utils::strdup(arg[3]+2);
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if (utils::strmatch(arg[3], "^v_")) {
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xstr = utils::strdup(arg[3] + 2);
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} else {
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ex = qe2f * utils::numeric(FLERR,arg[3],false,lmp);
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ex = qe2f * utils::numeric(FLERR, arg[3], false, lmp);
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xstyle = CONSTANT;
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}
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if (utils::strmatch(arg[4],"^v_")) {
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ystr = utils::strdup(arg[4]+2);
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if (utils::strmatch(arg[4], "^v_")) {
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ystr = utils::strdup(arg[4] + 2);
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} else {
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ey = qe2f * utils::numeric(FLERR,arg[4],false,lmp);
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ey = qe2f * utils::numeric(FLERR, arg[4], false, lmp);
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ystyle = CONSTANT;
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}
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if (utils::strmatch(arg[5],"^v_")) {
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zstr = utils::strdup(arg[5]+2);
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if (utils::strmatch(arg[5], "^v_")) {
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zstr = utils::strdup(arg[5] + 2);
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} else {
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ez = qe2f * utils::numeric(FLERR,arg[5],false,lmp);
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ez = qe2f * utils::numeric(FLERR, arg[5], false, lmp);
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zstyle = CONSTANT;
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}
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// optional args
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iregion = -1;
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idregion = nullptr;
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estr = nullptr;
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int iarg = 6;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield command");
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iregion = domain->find_region(arg[iarg+1]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix efield does not exist");
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idregion = utils::strdup(arg[iarg+1]);
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if (strcmp(arg[iarg], "region") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command");
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region = domain->get_region_by_id(arg[iarg + 1]);
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if (!region) error->all(FLERR, "Region {} for fix efield does not exist", arg[iarg + 1]);
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idregion = utils::strdup(arg[iarg + 1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"energy") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield command");
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if (utils::strmatch(arg[iarg+1],"^v_")) {
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estr = utils::strdup(arg[iarg+1]+2);
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} else error->all(FLERR,"Illegal fix efield command");
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} else if (strcmp(arg[iarg], "energy") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command");
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if (utils::strmatch(arg[iarg + 1], "^v_")) {
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estr = utils::strdup(arg[iarg + 1] + 2);
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} else
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error->all(FLERR, "Illegal fix efield command");
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iarg += 2;
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} else error->all(FLERR,"Illegal fix efield command");
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} else
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error->all(FLERR, "Illegal fix efield command");
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}
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force_flag = 0;
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fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
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maxatom = atom->nmax;
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memory->create(efield,maxatom,4,"efield:efield");
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memory->create(efield, maxatom, 4, "efield:efield");
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maxatom_energy = 0;
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}
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@ -118,11 +114,11 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
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FixEfield::~FixEfield()
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{
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delete [] xstr;
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delete [] ystr;
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delete [] zstr;
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delete [] estr;
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delete [] idregion;
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delete[] xstr;
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delete[] ystr;
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delete[] zstr;
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delete[] estr;
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delete[] idregion;
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memory->destroy(efield);
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}
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@ -144,74 +140,78 @@ void FixEfield::init()
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qflag = muflag = 0;
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if (atom->q_flag) qflag = 1;
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if (atom->mu_flag && atom->torque_flag) muflag = 1;
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if (!qflag && !muflag)
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error->all(FLERR,"Fix efield requires atom attribute q or mu");
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if (!qflag && !muflag) error->all(FLERR, "Fix efield requires atom attribute q or mu");
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// check variables
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if (xstr) {
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xvar = input->variable->find(xstr);
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if (xvar < 0)
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error->all(FLERR,"Variable name for fix efield does not exist");
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if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
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else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
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else error->all(FLERR,"Variable for fix efield is invalid style");
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if (xvar < 0) error->all(FLERR, "Variable {} for fix efield does not exist", xstr);
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if (input->variable->equalstyle(xvar))
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xstyle = EQUAL;
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else if (input->variable->atomstyle(xvar))
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xstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for fix efield is invalid style", xstr);
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}
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if (ystr) {
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yvar = input->variable->find(ystr);
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if (yvar < 0)
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error->all(FLERR,"Variable name for fix efield does not exist");
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if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
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else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
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else error->all(FLERR,"Variable for fix efield is invalid style");
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if (yvar < 0) error->all(FLERR, "Variable {} for fix efield does not exist", ystr);
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if (input->variable->equalstyle(yvar))
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ystyle = EQUAL;
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else if (input->variable->atomstyle(yvar))
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ystyle = ATOM;
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else
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error->all(FLERR, "Variable {} for fix efield is invalid style", ystr);
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}
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if (zstr) {
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zvar = input->variable->find(zstr);
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if (zvar < 0)
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error->all(FLERR,"Variable name for fix efield does not exist");
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if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
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else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
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else error->all(FLERR,"Variable for fix efield is invalid style");
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if (zvar < 0) error->all(FLERR, "Variable {} for fix efield does not exist", zstr);
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if (input->variable->equalstyle(zvar))
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zstyle = EQUAL;
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else if (input->variable->atomstyle(zvar))
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zstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for fix efield is invalid style", zstr);
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}
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if (estr) {
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evar = input->variable->find(estr);
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if (evar < 0)
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error->all(FLERR,"Variable name for fix efield does not exist");
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if (input->variable->atomstyle(evar)) estyle = ATOM;
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else error->all(FLERR,"Variable for fix efield is invalid style");
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} else estyle = NONE;
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if (evar < 0) error->all(FLERR, "Variable {} for fix efield does not exist", estr);
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if (input->variable->atomstyle(evar))
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estyle = ATOM;
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else
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error->all(FLERR, "Variable {} for fix efield is invalid style", estr);
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} else
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estyle = NONE;
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// set index and check validity of region
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if (iregion >= 0) {
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix aveforce does not exist");
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if (idregion) {
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region = domain->get_region_by_id(idregion);
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if (!region) error->all(FLERR, "Region {} for fix aveforce does not exist", idregion);
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}
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if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
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varflag = ATOM;
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else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
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varflag = EQUAL;
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else varflag = CONSTANT;
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else
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varflag = CONSTANT;
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if (muflag && varflag == ATOM)
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error->all(FLERR,"Fix efield with dipoles cannot use atom-style variables");
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error->all(FLERR, "Fix efield with dipoles cannot use atom-style variables");
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if (muflag && update->whichflag == 2 && comm->me == 0)
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error->warning(FLERR, "The minimizer does not re-orient dipoles when using fix efield");
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if (varflag == CONSTANT && estyle != NONE)
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error->all(FLERR,"Cannot use variable energy with "
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"constant efield in fix efield");
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if ((varflag == EQUAL || varflag == ATOM) &&
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update->whichflag == 2 && estyle == NONE)
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error->all(FLERR,"Must use variable energy with fix efield");
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error->all(FLERR, "Cannot use variable energy with constant efield in fix efield");
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if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE)
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error->all(FLERR, "Must use variable energy with fix efield");
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if (utils::strmatch(update->integrate_style,"^respa")) {
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ilevel_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels-1;
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if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
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if (utils::strmatch(update->integrate_style, "^respa")) {
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ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
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if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
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}
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}
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@ -219,12 +219,13 @@ void FixEfield::init()
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void FixEfield::setup(int vflag)
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{
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if (utils::strmatch(update->integrate_style,"^verlet"))
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if (utils::strmatch(update->integrate_style, "^respa")) {
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auto respa = dynamic_cast<Respa *>(update->integrate);
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respa->copy_flevel_f(ilevel_respa);
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post_force_respa(vflag, ilevel_respa, 0);
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respa->copy_f_flevel(ilevel_respa);
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} else {
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post_force(vflag);
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else {
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(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel_respa);
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post_force_respa(vflag,ilevel_respa,0);
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(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel_respa);
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}
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}
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@ -256,16 +257,12 @@ void FixEfield::post_force(int vflag)
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if (varflag == ATOM && atom->nmax > maxatom) {
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maxatom = atom->nmax;
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memory->destroy(efield);
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memory->create(efield,maxatom,4,"efield:efield");
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memory->create(efield, maxatom, 4, "efield:efield");
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}
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// update region if necessary
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Region *region = nullptr;
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if (iregion >= 0) {
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region = domain->regions[iregion];
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region->prematch();
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}
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if (region) region->prematch();
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// fsum[0] = "potential energy" for added force
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// fsum[123] = extra force added to atoms
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@ -274,7 +271,7 @@ void FixEfield::post_force(int vflag)
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force_flag = 0;
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double **x = atom->x;
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double fx,fy,fz;
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double fx, fy, fz;
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double v[6];
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// constant efield
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@ -288,27 +285,27 @@ void FixEfield::post_force(int vflag)
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if (qflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
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fx = q[i]*ex;
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fy = q[i]*ey;
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fz = q[i]*ez;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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fx = q[i] * ex;
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fy = q[i] * ey;
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fz = q[i] * ez;
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f[i][0] += fx;
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f[i][1] += fy;
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f[i][2] += fz;
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domain->unmap(x[i],image[i],unwrap);
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fsum[0] -= fx*unwrap[0]+fy*unwrap[1]+fz*unwrap[2];
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domain->unmap(x[i], image[i], unwrap);
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fsum[0] -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
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fsum[1] += fx;
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fsum[2] += fy;
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fsum[3] += fz;
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if (evflag) {
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v[0] = fx*unwrap[0];
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v[1] = fy*unwrap[1];
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v[2] = fz*unwrap[2];
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v[3] = fx*unwrap[1];
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v[4] = fx*unwrap[2];
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v[5] = fy*unwrap[2];
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v_tally(i,v);
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v[0] = fx * unwrap[0];
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v[1] = fy * unwrap[1];
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v[2] = fz * unwrap[2];
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v[3] = fx * unwrap[1];
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v[4] = fx * unwrap[2];
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v[5] = fy * unwrap[2];
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v_tally(i, v);
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}
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}
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}
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@ -319,38 +316,43 @@ void FixEfield::post_force(int vflag)
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if (muflag) {
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double **mu = atom->mu;
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double **t = atom->torque;
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double tx,ty,tz;
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double tx, ty, tz;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
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tx = ez*mu[i][1] - ey*mu[i][2];
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ty = ex*mu[i][2] - ez*mu[i][0];
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tz = ey*mu[i][0] - ex*mu[i][1];
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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tx = ez * mu[i][1] - ey * mu[i][2];
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ty = ex * mu[i][2] - ez * mu[i][0];
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tz = ey * mu[i][0] - ex * mu[i][1];
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t[i][0] += tx;
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t[i][1] += ty;
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t[i][2] += tz;
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fsum[0] -= mu[i][0]*ex + mu[i][1]*ey + mu[i][2]*ez;
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fsum[0] -= mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez;
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}
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}
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// variable efield, wrap with clear/add
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// potential energy = evar if defined, else 0.0
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// variable efield, wrap with clear/add
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// potential energy = evar if defined, else 0.0
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} else {
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modify->clearstep_compute();
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if (xstyle == EQUAL) ex = qe2f * input->variable->compute_equal(xvar);
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else if (xstyle == ATOM)
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input->variable->compute_atom(xvar,igroup,&efield[0][0],4,0);
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if (ystyle == EQUAL) ey = qe2f * input->variable->compute_equal(yvar);
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else if (ystyle == ATOM)
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input->variable->compute_atom(yvar,igroup,&efield[0][1],4,0);
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if (zstyle == EQUAL) ez = qe2f * input->variable->compute_equal(zvar);
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else if (zstyle == ATOM)
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input->variable->compute_atom(zvar,igroup,&efield[0][2],4,0);
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if (estyle == ATOM)
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input->variable->compute_atom(evar,igroup,&efield[0][3],4,0);
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if (xstyle == EQUAL) {
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ex = qe2f * input->variable->compute_equal(xvar);
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} else if (xstyle == ATOM) {
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input->variable->compute_atom(xvar, igroup, &efield[0][0], 4, 0);
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}
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if (ystyle == EQUAL) {
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ey = qe2f * input->variable->compute_equal(yvar);
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} else if (ystyle == ATOM) {
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input->variable->compute_atom(yvar, igroup, &efield[0][1], 4, 0);
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}
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if (zstyle == EQUAL) {
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ez = qe2f * input->variable->compute_equal(zvar);
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} else if (zstyle == ATOM) {
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input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0);
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}
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if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
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modify->addstep_compute(update->ntimestep + 1);
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@ -360,17 +362,26 @@ void FixEfield::post_force(int vflag)
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if (qflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
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if (xstyle == ATOM) fx = qe2f * q[i]*efield[i][0];
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else fx = q[i]*ex;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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if (xstyle == ATOM) {
|
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fx = qe2f * q[i] * efield[i][0];
|
||||
} else {
|
||||
fx = q[i] * ex;
|
||||
}
|
||||
f[i][0] += fx;
|
||||
fsum[1] += fx;
|
||||
if (ystyle == ATOM) fy = qe2f * q[i]*efield[i][1];
|
||||
else fy = q[i]*ey;
|
||||
if (ystyle == ATOM) {
|
||||
fy = qe2f * q[i] * efield[i][1];
|
||||
} else {
|
||||
fy = q[i] * ey;
|
||||
}
|
||||
f[i][1] += fy;
|
||||
fsum[2] += fy;
|
||||
if (zstyle == ATOM) fz = qe2f * q[i]*efield[i][2];
|
||||
else fz = q[i]*ez;
|
||||
if (zstyle == ATOM) {
|
||||
fz = qe2f * q[i] * efield[i][2];
|
||||
} else {
|
||||
fz = q[i] * ez;
|
||||
}
|
||||
f[i][2] += fz;
|
||||
fsum[3] += fz;
|
||||
if (estyle == ATOM) fsum[0] += efield[0][3];
|
||||
@ -383,13 +394,13 @@ void FixEfield::post_force(int vflag)
|
||||
if (muflag) {
|
||||
double **mu = atom->mu;
|
||||
double **t = atom->torque;
|
||||
double tx,ty,tz;
|
||||
double tx, ty, tz;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
|
||||
tx = ez*mu[i][1] - ey*mu[i][2];
|
||||
ty = ex*mu[i][2] - ez*mu[i][0];
|
||||
tz = ey*mu[i][0] - ex*mu[i][1];
|
||||
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
|
||||
tx = ez * mu[i][1] - ey * mu[i][2];
|
||||
ty = ex * mu[i][2] - ez * mu[i][0];
|
||||
tz = ey * mu[i][0] - ex * mu[i][1];
|
||||
t[i][0] += tx;
|
||||
t[i][1] += ty;
|
||||
t[i][2] += tz;
|
||||
@ -419,7 +430,7 @@ void FixEfield::min_post_force(int vflag)
|
||||
double FixEfield::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
|
||||
if (varflag == ATOM) bytes = atom->nmax * 4 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
@ -430,7 +441,7 @@ double FixEfield::memory_usage()
|
||||
double FixEfield::compute_scalar()
|
||||
{
|
||||
if (force_flag == 0) {
|
||||
MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
|
||||
force_flag = 1;
|
||||
}
|
||||
return fsum_all[0];
|
||||
@ -443,9 +454,8 @@ double FixEfield::compute_scalar()
|
||||
double FixEfield::compute_vector(int n)
|
||||
{
|
||||
if (force_flag == 0) {
|
||||
MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
|
||||
force_flag = 1;
|
||||
}
|
||||
return fsum_all[n+1];
|
||||
return fsum_all[n + 1];
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user