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

This commit is contained in:
Richard Berger 2019-04-30 01:39:19 -04:00
parent 66d94572e0 0005ee3e93
commit 7b7f405d2c
4 changed files with 44 additions and 10 deletions
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40
src/.gitignore vendored
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@ -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

8
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
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@ -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) *

4
src/MOLECULE/angle_table.cpp
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@ -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");
}

2
src/PYTHON/Install.sh
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@ -28,7 +28,7 @@ action () {
# force rebuild of files using python header
touch ../python.h
touch ../lmppython.h
# all package files with no dependencies