changed file names and added a lj12-5 function type in OPENMP pkg.

src/OPENMP/angle_spica_omp.cpp

@@ -17,32 +17,32 @@
 ------------------------------------------------------------------------- */
 
 #include "omp_compat.h"
-#include "angle_sdk_omp.h"
+#include "angle_spica_omp.h"
 #include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 
 #include "comm.h"
 #include "force.h"
-#include "lj_sdk_common.h"
+#include "lj_spica_common.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace LJSDKParms;
+using namespace LJSPICAParms;
 
 #define SMALL 0.001
 
 /* ---------------------------------------------------------------------- */
 
-AngleSDKOMP::AngleSDKOMP(class LAMMPS *lmp)
+AngleSPICAOMP::AngleSPICAOMP(class LAMMPS *lmp)
-  : AngleSDK(lmp), ThrOMP(lmp,THR_ANGLE)
+  : AngleSPICA(lmp), ThrOMP(lmp,THR_ANGLE)
 {
   suffix_flag |= Suffix::OMP;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void AngleSDKOMP::compute(int eflag, int vflag)
+void AngleSPICAOMP::compute(int eflag, int vflag)
 {
   ev_init(eflag,vflag);
 
@@ -81,7 +81,7 @@ void AngleSDKOMP::compute(int eflag, int vflag)
 }
 
 template <int EVFLAG, int EFLAG, int NEWTON_BOND>
-void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
+void AngleSPICAOMP::eval(int nfrom, int nto, ThrData * const thr)
 {
   int i1,i2,i3,n,type;
   double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3;
@@ -171,6 +171,13 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
 
           f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]);
           if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
+
+        } else if (ljt == LJ12_5) {
+          const double r5inv = r2inv*r2inv*sqrt(r2inv);
+          const double r7inv = r5inv*r2inv;
+
+          f13 = r5inv*(lj1[type1][type3]*r7inv - lj2[type1][type3]);
+          if (EFLAG) e13 = r5inv*(lj3[type1][type3]*r7inv - lj4[type1][type3]);
         }
 
         // make sure energy is 0.0 at the cutoff.

src/OPENMP/angle_spica_omp.h

@@ -17,22 +17,23 @@
 
 #ifdef ANGLE_CLASS
 // clang-format off
-AngleStyle(sdk/omp,AngleSDKOMP);
+AngleStyle(spica/omp,AngleSPICAOMP);
+AngleStyle(sdk/omp,AngleSPICAOMP);
 // clang-format on
 #else
 
-#ifndef LMP_ANGLE_SDK_OMP_H
+#ifndef LMP_ANGLE_SPICA_OMP_H
-#define LMP_ANGLE_SDK_OMP_H
+#define LMP_ANGLE_SPICA_OMP_H
 
-#include "angle_sdk.h"
+#include "angle_spica.h"
 #include "thr_omp.h"
 
 namespace LAMMPS_NS {
 
-class AngleSDKOMP : public AngleSDK, public ThrOMP {
+class AngleSPICAOMP : public AngleSPICA, public ThrOMP {
 
  public:
-  AngleSDKOMP(class LAMMPS *lmp);
+  AngleSPICAOMP(class LAMMPS *lmp);
   void compute(int, int) override;
 
  private:

src/OPENMP/pair_lj_spica_coul_long_omp.cpp

@@ -13,8 +13,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include "pair_lj_sdk_coul_long_omp.h"
+#include "pair_lj_spica_coul_long_omp.h"
-#include "lj_sdk_common.h"
+#include "lj_spica_common.h"
 
 #include "atom.h"
 #include "comm.h"
@@ -26,11 +26,11 @@
 
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
-using namespace LJSDKParms;
+using namespace LJSPICAParms;
 /* ---------------------------------------------------------------------- */
 
-PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) :
+PairLJSPICACoulLongOMP::PairLJSPICACoulLongOMP(LAMMPS *lmp) :
-  PairLJSDKCoulLong(lmp), ThrOMP(lmp, THR_PAIR)
+  PairLJSPICACoulLong(lmp), ThrOMP(lmp, THR_PAIR)
 {
   suffix_flag |= Suffix::OMP;
   respa_enable = 0;
@@ -38,7 +38,7 @@ PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) :
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJSDKCoulLongOMP::compute(int eflag, int vflag)
+void PairLJSPICACoulLongOMP::compute(int eflag, int vflag)
 {
   ev_init(eflag,vflag);
 
@@ -78,7 +78,7 @@ void PairLJSDKCoulLongOMP::compute(int eflag, int vflag)
 /* ---------------------------------------------------------------------- */
 
 template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
-void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
+void PairLJSPICACoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
 {
 
   const auto * _noalias const x = (dbl3_t *) atom->x[0];
@@ -195,6 +195,15 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
             if (EFLAG)
               evdwl = r6inv*(lj3[itype][jtype]*r6inv
                              - lj4[itype][jtype]) - offset[itype][jtype];
+
+          } else if (ljt == LJ12_5) {
+            const double r5inv = r2inv*r2inv*sqrt(r2inv);
+            const double r7inv = r5inv*r2inv;
+            forcelj = r5inv*(lj1[itype][jtype]*r7inv
+                             - lj2[itype][jtype]);
+            if (EFLAG)
+              evdwl = r5inv*(lj3[itype][jtype]*r7inv
+                             - lj4[itype][jtype]) - offset[itype][jtype];
           }
 
           if (sbindex) {
@@ -228,10 +237,10 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
 
 /* ---------------------------------------------------------------------- */
 
-double PairLJSDKCoulLongOMP::memory_usage()
+double PairLJSPICACoulLongOMP::memory_usage()
 {
   double bytes = memory_usage_thr();
-  bytes += PairLJSDKCoulLong::memory_usage();
+  bytes += PairLJSPICACoulLong::memory_usage();
 
   return bytes;
 }

src/OPENMP/pair_lj_spica_coul_long_omp.h

@@ -17,22 +17,23 @@
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(lj/sdk/coul/long/omp,PairLJSDKCoulLongOMP);
+PairStyle(lj/spica/coul/long/omp,PairLJSPICACoulLongOMP);
+PairStyle(lj/sdk/coul/long/omp,PairLJSPICACoulLongOMP);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_LJ_SDK_COUL_LONG_OMP_H
+#ifndef LMP_PAIR_LJ_SPICA_COUL_LONG_OMP_H
-#define LMP_PAIR_LJ_SDK_COUL_LONG_OMP_H
+#define LMP_PAIR_LJ_SPICA_COUL_LONG_OMP_H
 
-#include "pair_lj_sdk_coul_long.h"
+#include "pair_lj_spica_coul_long.h"
 #include "thr_omp.h"
 
 namespace LAMMPS_NS {
 
-class PairLJSDKCoulLongOMP : public PairLJSDKCoulLong, public ThrOMP {
+class PairLJSPICACoulLongOMP : public PairLJSPICACoulLong, public ThrOMP {
 
  public:
-  PairLJSDKCoulLongOMP(class LAMMPS *);
+  PairLJSPICACoulLongOMP(class LAMMPS *);
 
   void compute(int, int) override;
   double memory_usage() override;

src/OPENMP/pair_lj_spica_coul_msm_omp.cpp

@@ -14,8 +14,8 @@
    This style is a simplified re-implementation of the CG/CMM pair style
 ------------------------------------------------------------------------- */
 
-#include "pair_lj_sdk_coul_msm_omp.h"
+#include "pair_lj_spica_coul_msm_omp.h"
-#include "lj_sdk_common.h"
+#include "lj_spica_common.h"
 
 #include "atom.h"
 #include "comm.h"
@@ -29,11 +29,11 @@
 
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
-using namespace LJSDKParms;
+using namespace LJSPICAParms;
 /* ---------------------------------------------------------------------- */
 
-PairLJSDKCoulMSMOMP::PairLJSDKCoulMSMOMP(LAMMPS *lmp) :
+PairLJSPICACoulMSMOMP::PairLJSPICACoulMSMOMP(LAMMPS *lmp) :
-  PairLJSDKCoulMSM(lmp), ThrOMP(lmp, THR_PAIR)
+  PairLJSPICACoulMSM(lmp), ThrOMP(lmp, THR_PAIR)
 {
   suffix_flag |= Suffix::OMP;
   respa_enable = 0;
@@ -41,7 +41,7 @@ PairLJSDKCoulMSMOMP::PairLJSDKCoulMSMOMP(LAMMPS *lmp) :
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag)
+void PairLJSPICACoulMSMOMP::compute(int eflag, int vflag)
 {
   if (force->kspace->scalar_pressure_flag)
     error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' "
@@ -85,7 +85,7 @@ void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag)
 /* ---------------------------------------------------------------------- */
 
 template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
-void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr)
+void PairLJSPICACoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr)
 {
 
   const double * const * const x = atom->x;
@@ -194,6 +194,15 @@ void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr
             if (EFLAG)
               evdwl = r6inv*(lj3[itype][jtype]*r6inv
                              - lj4[itype][jtype]) - offset[itype][jtype];
+
+          } else if (ljt == LJ12_5) {
+            const double r5inv = r2inv*r2inv*sqrt(r2inv);
+            const double r7inv = r5inv*r2inv;
+            forcelj = r5inv*(lj1[itype][jtype]*r7inv
+                             - lj2[itype][jtype]);
+            if (EFLAG)
+              evdwl = r5inv*(lj3[itype][jtype]*r7inv
+                             - lj4[itype][jtype]) - offset[itype][jtype];
           }
 
           if (sbindex) {
@@ -227,10 +236,10 @@ void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr
 
 /* ---------------------------------------------------------------------- */
 
-double PairLJSDKCoulMSMOMP::memory_usage()
+double PairLJSPICACoulMSMOMP::memory_usage()
 {
   double bytes = memory_usage_thr();
-  bytes += PairLJSDKCoulMSM::memory_usage();
+  bytes += PairLJSPICACoulMSM::memory_usage();
 
   return bytes;
 }

src/OPENMP/pair_lj_spica_coul_msm_omp.h

@@ -17,22 +17,23 @@
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(lj/sdk/coul/msm/omp,PairLJSDKCoulMSMOMP);
+PairStyle(lj/spica/coul/msm/omp,PairLJSPICACoulMSMOMP);
+PairStyle(lj/sdk/coul/msm/omp,PairLJSPICACoulMSMOMP);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_LJ_SDK_COUL_MSM_OMP_H
+#ifndef LMP_PAIR_LJ_SPICA_COUL_MSM_OMP_H
-#define LMP_PAIR_LJ_SDK_COUL_MSM_OMP_H
+#define LMP_PAIR_LJ_SPICA_COUL_MSM_OMP_H
 
-#include "pair_lj_sdk_coul_msm.h"
+#include "pair_lj_spica_coul_msm.h"
 #include "thr_omp.h"
 
 namespace LAMMPS_NS {
 
-class PairLJSDKCoulMSMOMP : public PairLJSDKCoulMSM, public ThrOMP {
+class PairLJSPICACoulMSMOMP : public PairLJSPICACoulMSM, public ThrOMP {
 
  public:
-  PairLJSDKCoulMSMOMP(class LAMMPS *);
+  PairLJSPICACoulMSMOMP(class LAMMPS *);
 
   void compute(int, int) override;
   double memory_usage() override;

src/OPENMP/pair_lj_spica_omp.cpp

@@ -14,8 +14,8 @@
    This style is a simplified re-implementation of the CG/CMM pair style
 ------------------------------------------------------------------------- */
 
-#include "pair_lj_sdk_omp.h"
+#include "pair_lj_spica_omp.h"
-#include "lj_sdk_common.h"
+#include "lj_spica_common.h"
 
 #include "atom.h"
 #include "comm.h"
@@ -27,12 +27,12 @@
 
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
-using namespace LJSDKParms;
+using namespace LJSPICAParms;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJSDKOMP::PairLJSDKOMP(LAMMPS *lmp) :
+PairLJSPICAOMP::PairLJSPICAOMP(LAMMPS *lmp) :
-  PairLJSDK(lmp), ThrOMP(lmp, THR_PAIR)
+  PairLJSPICA(lmp), ThrOMP(lmp, THR_PAIR)
 {
   suffix_flag |= Suffix::OMP;
   respa_enable = 0;
@@ -40,7 +40,7 @@ PairLJSDKOMP::PairLJSDKOMP(LAMMPS *lmp) :
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJSDKOMP::compute(int eflag, int vflag)
+void PairLJSPICAOMP::compute(int eflag, int vflag)
 {
   ev_init(eflag,vflag);
 
@@ -80,7 +80,7 @@ void PairLJSDKOMP::compute(int eflag, int vflag)
 /* ---------------------------------------------------------------------- */
 
 template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
-void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
+void PairLJSPICAOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
 {
   int i,j,ii,jj,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -153,6 +153,15 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
           if (EFLAG)
             evdwl = r6inv*(lj3[itype][jtype]*r6inv
                            - lj4[itype][jtype]) - offset[itype][jtype];
+
+        } else if (ljt == LJ12_5) {
+          const double r5inv = r2inv*r2inv*sqrt(r2inv);
+          const double r7inv = r5inv*r2inv;
+          forcelj = r5inv*(lj1[itype][jtype]*r7inv
+                          - lj2[itype][jtype]);
+          if (EFLAG)
+            evdwl = r5inv*(lj3[itype][jtype]*r7inv
+                           - lj4[itype][jtype]) - offset[itype][jtype];
         } else continue;
 
         fpair = factor_lj*forcelj*r2inv;
@@ -179,10 +188,10 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
 
 /* ---------------------------------------------------------------------- */
 
-double PairLJSDKOMP::memory_usage()
+double PairLJSPICAOMP::memory_usage()
 {
   double bytes = memory_usage_thr();
-  bytes += PairLJSDK::memory_usage();
+  bytes += PairLJSPICA::memory_usage();
 
   return bytes;
 }

src/OPENMP/pair_lj_spica_omp.h

@@ -17,22 +17,23 @@
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(lj/sdk/omp,PairLJSDKOMP);
+PairStyle(lj/spica/omp,PairLJSPICAOMP);
+PairStyle(lj/sdk/omp,PairLJSPICAOMP);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_LJ_SDK_OMP_H
+#ifndef LMP_PAIR_LJ_SPICA_OMP_H
-#define LMP_PAIR_LJ_SDK_OMP_H
+#define LMP_PAIR_LJ_SPICA_OMP_H
 
-#include "pair_lj_sdk.h"
+#include "pair_lj_spica.h"
 #include "thr_omp.h"
 
 namespace LAMMPS_NS {
 
-class PairLJSDKOMP : public PairLJSDK, public ThrOMP {
+class PairLJSPICAOMP : public PairLJSPICA, public ThrOMP {
 
  public:
-  PairLJSDKOMP(class LAMMPS *);
+  PairLJSPICAOMP(class LAMMPS *);
 
   void compute(int, int) override;
   double memory_usage() override;

src/OPENMP/thr_omp.cpp

@@ -1042,7 +1042,7 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i
 }
 
 /* ----------------------------------------------------------------------
-   tally energy and virial from 1-3 repulsion of SDK angle into accumulators
+   tally energy and virial from 1-3 repulsion of SPICA angle into accumulators
 ------------------------------------------------------------------------- */
 
 void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,