SHAPES.cpp

/*
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "nonbonded/SHAPES.hpp"
 
#include <cmath>
#include <cstdio>
#include <cstring>
 
#include "nonbonded/LJ.hpp"
#include "utils/simError.h"
 
using namespace std;
namespace OpenMD {
 
  SHAPES::SHAPES() {
    initialized_ = false;
    lMax_        = 64;
    mMax_        = 64;
    forceField_  = NULL;
  }
 
  void SHAPES::initialize() {
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;
 
    // SHAPES handles all of the SHAPES-SHAPES interactions as well as
    // SHAPES-LJ cross interactions:
 
    for (at = atomTypes->beginType(i); at != NULL;
         at = atomTypes->nextType(i)) {
      if (at->isShape()) addShape(dynamic_cast<ShapeAtomType*>(at));
 
      if (at->isLennardJones()) addLJ(at);
    }
 
    initialized_ = true;
  }
 
  void SHAPES::addShape(ShapeAtomType* atomType) {
    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();
 
    if (atomType->isShape()) {
      pair<map<int, ShapeAtomType*>::iterator, bool> ret;
      ret = ShapesMap.insert(pair<int, ShapeAtomType*>(atp.ident, atomType));
      if (ret.second == false) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "SHAPES already had a previous entry with ident %d\n",
                 atp.ident);
        painCave.severity = OPENMD_INFO;
        painCave.isFatal  = 0;
        simError();
      }
 
      ShapesMap.insert(pair<int, ShapeAtomType*>(
          atp.ident, static_cast<ShapeAtomType*>(atomType)));
 
    } else if (atomType->isLennardJones()) {
      RealType d1 = getLJSigma(atomType) / sqrt(2.0);
      RealType e1 = getLJEpsilon(atomType);
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SHAPES::addType was passed an atomType (%s) that does not\n"
               "\tappear to be a SHAPES or Lennard-Jones atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
  }
 
  LJParam SHAPES::getLJParam(AtomType* atomType) {
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isLennardJones()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SHAPES::getLJParam was passed an atomType (%s) that does not\n"
               "\tappear to be a Lennard-Jones atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    GenericData* data = atomType->getPropertyByName("LennardJones");
    if (data == NULL) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SHAPES::getLJParam could not find Lennard-Jones\n"
               "\tparameters for atomType %s.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
    if (ljData == NULL) {
      snprintf(
          painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
          "SHAPES::getLJParam could not convert GenericData to LJParam for\n"
          "\tatom type %s\n",
          atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    return ljData->getData();
  }
 
  RealType SHAPES::getLJEpsilon(AtomType* atomType) {
    LJParam ljParam = getLJParam(atomType);
    return ljParam.epsilon;
  }
  RealType SHAPES::getLJSigma(AtomType* atomType) {
    LJParam ljParam = getLJParam(atomType);
    return ljParam.sigma;
  }
 
  RealType SHAPES::getGayBerneCut(int atid) {
    if (!initialized_) initialize();
    std::map<int, AtomType*>::const_iterator it;
    it = SHAPESMap.find(atid);
    if (it == SHAPESMap.end()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SHAPES::getGayBerneCut could not find atid %d in SHAPESMap\n",
               (atid));
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    AtomType* atype = it->second;
 
    RealType gbCut;
 
    if (atype->isGayBerne()) {
      GayBerneParam gb = getGayBerneParam(atype);
 
      // sigma is actually sqrt(2) * l for prolate ellipsoids
      gbCut = 2.5 * sqrt(2.0) * max(gb.SHAPES_l, gb.SHAPES_d);
 
    } else if (atype->isLennardJones()) {
      gbCut = 2.5 * LJ::Instance()->getSigma(atype);
    }
 
    return gbCut;
  }
 
  void SHAPES::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType r,
                         RealType r2, RealType sw, RealType& vpair,
                         RealType& pot, RotMat3x3d A1, RotMat3x3d A2,
                         Vector3d& f1, Vector3d& t1, Vector3d& t2) {
    if (!initialized_) initialize();
 
    pair<AtomType*, AtomType*> key = make_pair(at1, at2);
    SHAPESInteractionData mixer    = MixingMap[key];
 
    RealType r3 = r2 * r;
    RealType r5 = r3 * r2;
 
    Vector3d drdi  = -d / r;
    Vector3d drdui = V3Zero;
    Vector3d drdj  = d / r;
    Vector3d drduj = V3Zero;
 
    bool i_is_LJ = at1->isLennardJones();
    bool j_is_LJ = at2->isLennardJones();
 
    RealType sigma_i;
    RealType s_i;
    RealType eps_i;
    Vector3d dsigmaidr;
    Vector3d disgmaidu;
    Vector3d dsidr;
    Vector3d dsidu;
    Vector3d depsidr;
    Vector3d depsidu;
 
    if (i_is_LJ) {
      sigma_i   = LJ::Instance()->getSigma(at1);
      s_i       = sigma_i;
      epsilon_i = LJ::Instance()->getEpsilon(at1);
      dsigmaidr = V3Zero;
      dsigmaidu = V3Zero;
      dsidr     = V3Zero;
      dsidu     = V3Zero;
      depsidr   = V3Zero;
      depsidu   = V3Zero;
    } else {
      // rotate the inter-particle separation into the two different
      // body-fixed coordinate systems:
 
      Vector3d ri = A1 * d;
 
      RealType xi  = ri.x() / r;
      RealType yi  = ri.y() / r;
      RealType zi  = ri.z() / r;
      RealType xi2 = xi * xi;
      RealType yi2 = yi * yi;
      RealType zi2 = zi * zi;
      RealType cti = zi / r;
 
      if (cti > 1.0) cti = 1.0;
      if (cti < -1.0_dp) cti = -1.0;
 
      Vector3d dctidr(-zi * xi / r3, -zi * yi / r3, 1.0 / r - zi2 / r3);
 
      Vector3d dctidu(yi / r, -zi / r, 0.0);
 
      // this is an attempt to try to truncate the singularity when
      // sin(theta) is near 0.0:
 
      RealType sti2 = 1.0 - cti * cti;
      RealType proji;
      Vector3d dcpidr, dcpidu, dspidr, dspidu;
      if (fabs(sti2) < 1.0e-12) {
        proji  = sqrt(r * 1.0e-12);
        dcpidr = Vector3d(1.0 / proji, 0.0, 0.0);
        dcpidu = Vector3d(xi / proji, 0.0, 0.0);
        dspidr = Vector3d(0.0, 1.0 / proji, 0.0);
        dspidu = Vector3d(0.0, yi / proji, 0.0);
      } else {
        proji           = sqrt(xi2 + yi2);
        RealType proji3 = proji * proji * proji;
        dcpidr =
            Vector3d(1.0_dp / proji - xi2 / proji3, -xi * yi / proji3, 0.0);
        dcpidu = Vector3d(xi / proji - (xi2 * xi) / proji3,
                          -(xi * yi2) / proji3, 0.0);
        dspidr =
            Vector3d(-xi * yi / proji3, 1.0_dp / proji - yi2 / proji3, 0.0);
        dspidu = Vector3d(-(yi * xi2) / proji3,
                          yi / proji - (yi2 * yi) / proji3, 0.0);
      }
 
      cpi        = xi / proji;
      dcpidr.z() = 0.0;
      dcpidu.z() = 0.0;
 
      spi        = yi / proji;
      dspidr.z() = 0.0;
      dspidu.z() = 0.0;
 
      RealType sigma0 = mixer.sigma0;
      RealType dw     = mixer.dw;
      RealType eps0   = mixer.eps0;
      RealType x2     = mixer.x2;
      RealType xa2    = mixer.xa2;
      RealType xai2   = mixer.xai2;
      RealType xp2    = mixer.xp2;
      RealType xpap2  = mixer.xpap2;
      RealType xpapi2 = mixer.xpapi2;
 
      Vector3d ul1 = A1.getRow(2);
      Vector3d ul2 = A2.getRow(2);
 
      RealType a, b, g;
 
      if (i_is_LJ) {
        a   = 0.0;
        ul1 = V3Zero;
      } else {
        a = dot(d, ul1);
      }
 
      if (j_is_LJ) {
        b   = 0.0;
        ul2 = V3Zero;
      } else {
        b = dot(d, ul2);
      }
 
      if (i_is_LJ || j_is_LJ)
        g = 0.0;
      else
        g = dot(ul1, ul2);
 
      RealType au = a / r;
      RealType bu = b / r;
 
      RealType au2 = au * au;
      RealType bu2 = bu * bu;
      RealType g2  = g * g;
 
      RealType H =
          (xa2 * au2 + xai2 * bu2 - 2.0 * x2 * au * bu * g) / (1.0 - x2 * g2);
      RealType Hp = (xpap2 * au2 + xpapi2 * bu2 - 2.0 * xp2 * au * bu * g) /
                    (1.0 - xp2 * g2);
 
      RealType sigma = sigma0 / sqrt(1.0 - H);
      RealType e1    = 1.0 / sqrt(1.0 - x2 * g2);
      RealType e2    = 1.0 - Hp;
      RealType eps   = eps0 * pow(e1, nu_) * pow(e2, mu_);
      RealType BigR  = dw * sigma0 / (r - sigma + dw * sigma0);
 
      RealType R3  = BigR * BigR * BigR;
      RealType R6  = R3 * R3;
      RealType R7  = R6 * BigR;
      RealType R12 = R6 * R6;
      RealType R13 = R6 * R7;
 
      RealType U = vdwMult * 4.0 * eps * (R12 - R6);
 
      RealType s3  = sigma * sigma * sigma;
      RealType s03 = sigma0 * sigma0 * sigma0;
 
      RealType pref1 = -vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * r);
 
      RealType pref2 =
          vdwMult * 8.0 * eps * s3 * (6.0 * R13 - 3.0 * R7) / (dw * r * s03);
 
      RealType dUdr = -(pref1 * Hp + pref2 * (sigma0 * sigma0 * r / s3 + H));
 
      RealType dUda = pref1 * (xpap2 * au - xp2 * bu * g) / (1.0 - xp2 * g2) +
                      pref2 * (xa2 * au - x2 * bu * g) / (1.0 - x2 * g2);
 
      RealType dUdb = pref1 * (xpapi2 * bu - xp2 * au * g) / (1.0 - xp2 * g2) +
                      pref2 * (xai2 * bu - x2 * au * g) / (1.0 - x2 * g2);
 
      RealType dUdg =
          4.0 * eps * nu_ * (R12 - R6) * x2 * g / (1.0 - x2 * g2) +
          8.0 * eps * mu_ * (R12 - R6) * (xp2 * au * bu - Hp * xp2 * g) /
              (1.0 - xp2 * g2) / e2 +
          8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) *
              (x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03);
 
      Vector3d rhat = d / r;
      Vector3d rxu1 = cross(d, ul1);
      Vector3d rxu2 = cross(d, ul2);
      Vector3d uxu  = cross(ul1, ul2);
 
      pot += U * sw;
      f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2;
      t1 += dUda * rxu1 - dUdg * uxu;
      t2 += dUdb * rxu2 - dUdg * uxu;
      vpair += U * sw;
 
      return;
    }
  }
}  // namespace OpenMD