From 035279de8762d4ab8c40b4b2ae6b1f4340278d75 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 1 Oct 2016 06:26:14 -0400 Subject: [PATCH 1/4] correct logic bug in bufix for fix tmd (cherry picked from commit 267c1ec95783782a7a15132921a9f62737311d18) --- src/fix_tmd.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 8d25739f61..f5ed970da7 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -460,9 +460,9 @@ void FixTMD::readfile(char *file) else n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z); - if (n < 0 && me == 0) { - error->warning(FLERR,"Ignoring empty or incorrectly formatted" - " line in target file"); + if (n < 0) { + if (me == 0) error->warning(FLERR,"Ignoring empty or incorrectly" + " formatted line in target file"); bufptr = next + 1; continue; } From a3e05a2bac7d7756bd26d9e1b976a671208895f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 1 Oct 2016 06:34:45 -0400 Subject: [PATCH 2/4] permission cleanup --- lib/linalg/Makefile.gfortran | 0 lib/linalg/Makefile.mingw32-cross | 0 lib/linalg/Makefile.mingw64-cross | 0 lib/meam/Makefile.tbird | 0 lib/meam/meam_data.F | 0 lib/meam/meam_dens_final.F | 0 lib/meam/meam_dens_init.F | 0 lib/meam/meam_force.F | 0 lib/meam/meam_setup_done.F | 0 lib/meam/meam_setup_global.F | 0 lib/meam/meam_setup_param.F | 0 lib/reax/Makefile.g95 | 0 lib/reax/Makefile.gfortran | 0 src/MANYBODY/pair_vashishta_table.cpp | 0 src/MANYBODY/pair_vashishta_table.h | 0 15 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 lib/linalg/Makefile.gfortran mode change 100755 => 100644 lib/linalg/Makefile.mingw32-cross mode change 100755 => 100644 lib/linalg/Makefile.mingw64-cross mode change 100755 => 100644 lib/meam/Makefile.tbird mode change 100755 => 100644 lib/meam/meam_data.F mode change 100755 => 100644 lib/meam/meam_dens_final.F mode change 100755 => 100644 lib/meam/meam_dens_init.F mode change 100755 => 100644 lib/meam/meam_force.F mode change 100755 => 100644 lib/meam/meam_setup_done.F mode change 100755 => 100644 lib/meam/meam_setup_global.F mode change 100755 => 100644 lib/meam/meam_setup_param.F mode change 100755 => 100644 lib/reax/Makefile.g95 mode change 100755 => 100644 lib/reax/Makefile.gfortran mode change 100755 => 100644 src/MANYBODY/pair_vashishta_table.cpp mode change 100755 => 100644 src/MANYBODY/pair_vashishta_table.h diff --git a/lib/linalg/Makefile.gfortran b/lib/linalg/Makefile.gfortran old mode 100755 new mode 100644 diff --git a/lib/linalg/Makefile.mingw32-cross b/lib/linalg/Makefile.mingw32-cross old mode 100755 new mode 100644 diff --git a/lib/linalg/Makefile.mingw64-cross b/lib/linalg/Makefile.mingw64-cross old mode 100755 new mode 100644 diff --git a/lib/meam/Makefile.tbird b/lib/meam/Makefile.tbird old mode 100755 new mode 100644 diff --git a/lib/meam/meam_data.F b/lib/meam/meam_data.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_dens_final.F b/lib/meam/meam_dens_final.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_dens_init.F b/lib/meam/meam_dens_init.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_force.F b/lib/meam/meam_force.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_setup_global.F b/lib/meam/meam_setup_global.F old mode 100755 new mode 100644 diff --git a/lib/meam/meam_setup_param.F b/lib/meam/meam_setup_param.F old mode 100755 new mode 100644 diff --git a/lib/reax/Makefile.g95 b/lib/reax/Makefile.g95 old mode 100755 new mode 100644 diff --git a/lib/reax/Makefile.gfortran b/lib/reax/Makefile.gfortran old mode 100755 new mode 100644 diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp old mode 100755 new mode 100644 diff --git a/src/MANYBODY/pair_vashishta_table.h b/src/MANYBODY/pair_vashishta_table.h old mode 100755 new mode 100644 From 1985db4fb1529b7b05f0a2c87bf536871b601850 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 1 Oct 2016 23:05:05 -0400 Subject: [PATCH 3/4] correct designation of meam supporting USER-OMP and meam/spline not --- doc/src/Section_commands.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 91ec679360..8f36c3c98a 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -896,7 +896,7 @@ KOKKOS, o = USER-OMP, t = OPT. "lubricate/poly (o)"_pair_lubricate.html, "lubricateU"_pair_lubricateU.html, "lubricateU/poly"_pair_lubricateU.html, -"meam (o)"_pair_meam.html, +"meam"_pair_meam.html, "mie/cut (o)"_pair_mie.html, "morse (got)"_pair_morse.html, "nb3b/harmonic (o)"_pair_nb3b_harmonic.html, @@ -956,7 +956,7 @@ package"_Section_start.html#start_3. "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, "lj/sf (o)"_pair_lj_sf.html, -"meam/spline"_pair_meam_spline.html, +"meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, "morse/smooth/linear"_pair_morse.html, From 03766dbda76f854d94e86ba5ab7107bb5a869bf0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 3 Oct 2016 16:28:59 -0400 Subject: [PATCH 4/4] apply bugfix for MEAM provided by Wolfgang Verestek on lammps-users this closes lammps/#188 --- lib/meam/meam_setup_done.F | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F index 0684fde70b..8c22f4ca89 100644 --- a/lib/meam/meam_setup_done.F +++ b/lib/meam/meam_setup_done.F @@ -183,6 +183,16 @@ c real*8, external :: zbl real*8, external :: compute_phi +c check for previously allocated arrays and free them + if(allocated(phir)) deallocate(phir) + if(allocated(phirar)) deallocate(phirar) + if(allocated(phirar1)) deallocate(phirar1) + if(allocated(phirar2)) deallocate(phirar2) + if(allocated(phirar3)) deallocate(phirar3) + if(allocated(phirar4)) deallocate(phirar4) + if(allocated(phirar5)) deallocate(phirar5) + if(allocated(phirar6)) deallocate(phirar6) + c allocate memory for array that defines the potential allocate(phir(nr,(neltypes*(neltypes+1))/2))