From aa11935e88d0776e71bfae8fb4055a4711ce5ff9 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Mon, 11 Jul 2022 11:38:31 +0900 Subject: [PATCH] updated .gitignore and Purge.list, and author info, and added URL to the SPICA web. --- doc/src/Packages_details.rst | 5 ++++- doc/src/pair_spica.rst | 1 + src/.gitignore | 18 +++++++++--------- src/CG-SPICA/README | 11 ++++------- src/Purge.list | 24 ++++++++++++++++++++++++ 5 files changed, 42 insertions(+), 17 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 24a8cc11b9..d1b69740ce 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -376,7 +376,9 @@ Several pair styles and an angle style which implement the coarse-grained SPICA (formerly called SDK) model which enables simulation of biological or soft material systems. -**Author:** Axel Kohlmeyer (Temple U). +**Original Author:** Axel Kohlmeyer (Temple U). + +**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U). **Supporting info:** @@ -386,6 +388,7 @@ simulation of biological or soft material systems. * :doc:`angle_style spica ` * examples/PACKAGES/cgspica * https://www.lammps.org/pictures.html#cg +* https://www.spica-ff.org/ ---------- diff --git a/doc/src/pair_spica.rst b/doc/src/pair_spica.rst index 9bd6ee069c..eac44ad0f2 100644 --- a/doc/src/pair_spica.rst +++ b/doc/src/pair_spica.rst @@ -82,6 +82,7 @@ given by as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in :ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `. Rc is the cutoff. +Summary information on these force fields can be found at https://www.spica-ff.org Style *lj/spica/coul/long* computes the adds Coulombic interactions with an additional damping factor applied so it can be used in diff --git a/src/.gitignore b/src/.gitignore index 4c1cf49b3b..b783a07892 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -409,8 +409,8 @@ /angle_mm3.h /angle_quartic.cpp /angle_quartic.h -/angle_sdk.cpp -/angle_sdk.h +/angle_spica.cpp +/angle_spica.h /angle_table.cpp /angle_table.h /atom_vec_angle.cpp @@ -990,7 +990,7 @@ /improper_umbrella.h /interlayer_taper.h /kissfft.h -/lj_sdk_common.h +/lj_spica_common.h /math_complex.h /math_vector.h /message.cpp @@ -1218,12 +1218,12 @@ /pair_lj_long_tip4p_long.h /pair_lj_cut_tgpu.cpp /pair_lj_cut_tgpu.h -/pair_lj_sdk.cpp -/pair_lj_sdk.h -/pair_lj_sdk_coul_long.cpp -/pair_lj_sdk_coul_long.h -/pair_lj_sdk_coul_msm.cpp -/pair_lj_sdk_coul_msm.h +/pair_lj_spica.cpp +/pair_lj_spica.h +/pair_lj_spica_coul_long.cpp +/pair_lj_spica_coul_long.h +/pair_lj_spica_coul_msm.cpp +/pair_lj_spica_coul_msm.h /pair_lj_sf_dipole_sf.cpp /pair_lj_sf_dipole_sf.h /pair_lj_switch3_coulgauss_long.cpp diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README index cbef4ef2c9..1ba2274e57 100644 --- a/src/CG-SPICA/README +++ b/src/CG-SPICA/README @@ -38,18 +38,15 @@ style, since the number of charged atom types is usually small. To exploit this property, the use of the kspace_style pppm/cg is recommended over regular pppm. -The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. - -The person who added a new function type (LJ12_5) to this package is -Yusuke Miyazaki at Okayama U (ymiyazaki93 at gmail.com). Contact him -if you have questions about his code. +Original Author: Axel Kohlmeyer (akohlmey at gmail.com) at Temple U . +Maintainers : Yusuke Miyazaki (ymiyazaki93 at gmail.com) and + Wataru Shinoda (shinoda at okayama-u.ac.jp) at Okayama U. +Contact them if you have questions about his code. --------------------------------- Thanks for contributions, support and testing goes to -Wataru Shinoda (Okayama University) Russell DeVane (Procter & Gamble) Michael L. Klein (Temple University, Philadelphia) Balasubramanian Sundaram (JNCASR, Bangalore) diff --git a/src/Purge.list b/src/Purge.list index a2fa9f1165..5b838be535 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -51,6 +51,30 @@ lmpinstalledpkgs.h lmpgitversion.h mliap_model_python_couple.cpp mliap_model_python_couple.h +# renamed on 11 July 2022 +lj_sdk_common.h +angle_sdk.cpp +pair_lj_sdk.cpp +pair_lj_sdk_coul_msm.cpp +pair_lj_sdk_coul_long.h +pair_lj_sdk_coul_msm.h +angle_sdk.h +pair_lj_sdk.h +pair_lj_sdk_coul_long.cpp +pair_lj_sdk_kokkos.h +pair_lj_sdk_kokkos.cpp +pair_lj_sdk_gpu.cpp +pair_lj_sdk_gpu.h +pair_lj_sdk_coul_long_gpu.cpp +pair_lj_sdk_coul_long_gpu.h +pair_lj_sdk_omp.h +pair_lj_sdk_coul_msm_omp.cpp +pair_lj_sdk_coul_long_omp.h +angle_sdk_omp.cpp +pair_lj_sdk_omp.cpp +pair_lj_sdk_coul_msm_omp.h +pair_lj_sdk_coul_long_omp.cpp +angle_sdk_omp.h # removed on 8 April 2022 fix_client_md.cpp fix_client_md.h