Commit 7b7f405d authored by Richard Berger's avatar Richard Berger
Browse files

Merge remote-tracking branch 'origin/master' into gpu_opencl_bugfixes

parents 66d94572 0005ee3e

src/.gitignore

+38 −2
Original line number Diff line number Diff line
@@ -150,10 +150,16 @@ 
/compute_spin.h

/fix_langevin_spin.cpp

/fix_langevin_spin.h

/fix_neb_spin.cpp

/fix_neb_spin.h

/fix_nve_spin.cpp

/fix_nve_spin.h

/fix_precession_spin.cpp

/fix_precession_spin.h

/min_spin.cpp

/min_spin.h

/neb_spin.cpp

/neb_spin.h

/pair_spin.cpp

/pair_spin.h

/pair_spin_dmi.cpp
@@ -187,6 +193,8 @@ 
/angle_cosine_shift_exp.h

/angle_cosine_squared.cpp

/angle_cosine_squared.h

/angle_cross.cpp

/angle_cross.h

/angle_dipole.cpp

/angle_dipole.h

/angle_fourier.cpp
@@ -195,6 +203,8 @@ 
/angle_fourier_simple.h

/angle_harmonic.cpp

/angle_harmonic.h

/angle_mm3.cpp

/angle_mm3.h

/angle_quartic.cpp

/angle_quartic.h

/angle_sdk.cpp
@@ -249,6 +259,8 @@ 
/bond_harmonic_shift.h

/bond_harmonic_shift_cut.cpp

/bond_harmonic_shift_cut.h

/bond_mm3.cpp

/bond_mm3.h

/bond_morse.cpp

/bond_morse.h

/bond_nonlinear.cpp
@@ -377,6 +389,8 @@ 
/dihedral_table.h

/dihedral_table_cut.cpp

/dihedral_table_cut.h

/dump_atom_adios.cpp

/dump_atom_adios.h

/dump_atom_gz.cpp

/dump_atom_gz.h

/dump_xyz_gz.cpp
@@ -387,6 +401,8 @@ 
/dump_cfg_gz.h

/dump_cfg_mpiio.cpp

/dump_cfg_mpiio.h

/dump_custom_adios.cpp

/dump_custom_adios.h

/dump_custom_gz.cpp

/dump_custom_gz.h

/dump_custom_mpiio.cpp
@@ -403,6 +419,8 @@ 
/dump_xtc.h

/dump_xyz_mpiio.cpp

/dump_xyz_mpiio.h

/dynamical_matrix.cpp

/dynamical_matrix.h

/ewald.cpp

/ewald.h

/ewald_cg.cpp
@@ -445,6 +463,8 @@ 
/fix_dpd_energy.h

/fix_efield.cpp

/fix_efield.h

/fix_electron_stopping.cpp

/fix_electron_stopping.h

/fix_eos_cv.cpp

/fix_eos_cv.h

/fix_eos_table.cpp
@@ -683,6 +703,10 @@ 
/improper_cvff.h

/improper_distance.cpp

/improper_distance.h

/improper_distharm.cpp

/improper_distharm.h

/improper_sqdistharm.cpp

/improper_sqdistharm.h

/improper_fourier.cpp

/improper_fourier.h

/improper_harmonic.cpp
@@ -805,6 +829,8 @@ 
/pair_gauss_cut.h

/pair_gayberne.cpp

/pair_gayberne.h

/pair_granular.cpp

/pair_granular.h

/pair_gran_easy.cpp

/pair_gran_easy.h

/pair_gran_hertz_history.cpp
@@ -829,6 +855,8 @@ 
/pair_kolmogorov_crespi_z.h

/pair_lcbop.cpp

/pair_lcbop.h

/pair_lebedeva_z.cpp

/pair_lebedeva_z.h

/pair_line_lj.cpp

/pair_line_lj.h

/pair_list.cpp
@@ -847,8 +875,14 @@ 
/pair_lj_class2.h

/pair_lj_class2_coul_cut.cpp

/pair_lj_class2_coul_cut.h

/pair_lj_class2_coul_cut_soft.cpp

/pair_lj_class2_coul_cut_soft.h

/pair_lj_class2_coul_long.cpp

/pair_lj_class2_coul_long.h

/pair_lj_class2_coul_long_soft.cpp

/pair_lj_class2_coul_long_soft.h

/pair_lj_class2_soft.cpp

/pair_lj_class2_soft.h

/pair_lj_coul.cpp

/pair_lj_coul.h

/pair_coul_cut_soft.cpp
@@ -893,6 +927,8 @@ 
/pair_lj_sdk_coul_msm.h

/pair_lj_sf_dipole_sf.cpp

/pair_lj_sf_dipole_sf.h

/pair_lj_switch3_coulgauss_long.cpp

/pair_lj_switch3_coulgauss_long.h

/pair_lubricateU.cpp

/pair_lubricateU.h

/pair_lubricateU_poly.cpp
@@ -901,12 +937,12 @@ 
/pair_lubricate_poly.h

/pair_lubricate.cpp

/pair_lubricate.h

/pair_meam.cpp

/pair_meam.h

/pair_meam_spline.cpp

/pair_meam_spline.h

/pair_meam_sw_spline.cpp

/pair_meam_sw_spline.h

/pair_mm3_switch3_coulgauss_long.cpp

/pair_mm3_switch3_coulgauss_long.h

/pair_morse_soft.cpp

/pair_morse_soft.h

/pair_nb3b_harmonic.cpp

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

+3 −5
Original line number Diff line number Diff line
@@ -501,6 +501,7 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) 


      if (rsq < cut_bothsq) {

        r2inv = 1.0/rsq;

        r6inv = r2inv*r2inv*r2inv;



        if (rsq < cut_coulsq) {

          if (!ncoultablebits || rsq <= tabinnersq) {
@@ -541,7 +542,6 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) 
        } else forcecoul = 0.0;



        if (rsq < cut_ljsq && rsq > cut_in_off_sq) {

          r6inv = r2inv*r2inv*r2inv;

          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);

          if (rsq > cut_lj_innersq) {

            switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
@@ -582,11 +582,10 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) 
          } else ecoul = 0.0;



          if (rsq < cut_ljsq) {

            r6inv = r2inv*r2inv*r2inv;

            evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);

            if (rsq > cut_lj_innersq) {

              rinv = 1.0/r;

              r3inv = rinv*rinv*rinv;

              rinv = sqrt(r2inv);

              r3inv = r2inv*rinv;

              evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *

                (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);

              evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
@@ -620,7 +619,6 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) 
          } else forcecoul = 0.0;



          if (rsq <= cut_in_off_sq) {

            r6inv = r2inv*r2inv*r2inv;

            forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);

            if (rsq > cut_lj_innersq) {

              switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *

src/MOLECULE/angle_table.cpp

+2 −2
Original line number Diff line number Diff line
@@ -500,7 +500,7 @@ void AngleTable::param_extract(Table *tb, char *line) 
{

  tb->ninput = 0;

  tb->fpflag = 0;

  tb->theta0 = 180.0;

  tb->theta0 = MY_PI;



  char *word = strtok(line," \t\n\r\f");

  while (word) {
@@ -517,7 +517,7 @@ void AngleTable::param_extract(Table *tb, char *line) 
      tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI);

    } else if (strcmp(word,"EQ") == 0) {

      word = strtok(NULL," \t\n\r\f");

      tb->theta0 = atof(word);

      tb->theta0 = atof(word)/180.0*MY_PI;

    } else {

      error->one(FLERR,"Invalid keyword in angle table parameters");

    }

src/PYTHON/Install.sh

+1 −1
Original line number Diff line number Diff line
@@ -28,7 +28,7 @@ action () { 


# force rebuild of files using python header



touch ../python.h

touch ../lmppython.h



# all package files with no dependencies

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