diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 8691951f10..bd62ec3e7b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -7,8 +7,12 @@ unit-tests: script: - echo "Installing dependencies" - apt-get update - - apt-get install -y cmake make gcc g++ gfortran python3 python3-numpy libblas-dev liblapack-dev + - apt-get install -y cmake make gcc g++ gfortran python3 python3-numpy python3-yaml libblas-dev liblapack-dev - base_dir=$PWD + - echo "Checking code style" + - python3 ./tools/coding_standard/homepage.py . + - python3 ./tools/coding_standard/whitespace.py . + - python3 ./tools/coding_standard/permissions.py . - echo "Building lammps in directory $base_dir" - mkdir build && cd build - cmake ../cmake @@ -26,13 +30,13 @@ unit-tests: - adduser tester - chown -R tester $base_dir - runuser -u tester ctest - - echo "running tests in examples/electrode subdirectory of $base_dir" + - echo "running tests in examples/PACKAGES/electrode subdirectory of $base_dir" - lmpbin=$base_dir/build/lmp - - cd $base_dir/examples/electrode/check_amat/ + - cd $base_dir/examples/PACKAGES/electrode/check_amat/ - bash check.sh $lmpbin - - cd $base_dir/examples/electrode/check_etypes/ + - cd $base_dir/examples/PACKAGES/electrode/check_etypes/ - bash check.sh $lmpbin - - cd $base_dir/examples/electrode/check_ffield/ + - cd $base_dir/examples/PACKAGES/electrode/check_ffield/ - bash check.sh $lmpbin - - cd $base_dir/examples/electrode/check_intel/ + - cd $base_dir/examples/PACKAGES/electrode/check_intel/ - bash check.sh $lmpbin diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 72790f238f..fef714f942 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1291,7 +1291,7 @@ be built for the most part with all major versions of the C++ language. .. _electrode: -ELECTRODE package +ELECTRODE package ----------------- This package depends on the KSPACE package. diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 7b31f56b46..26595c1d38 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -66,9 +66,6 @@ OPT. * :doc:`edpd/source ` * :doc:`efield ` * :doc:`ehex ` - * :doc:`electrode/conp ` - * :doc:`electrode/conq ` - * :doc:`electrode/thermo ` * :doc:`electrode/conp (i) ` * :doc:`electrode/conq (i) ` * :doc:`electrode/thermo (i) ` diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index efaa321f7d..0f64338415 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -42,6 +42,5 @@ OPT. * :doc:`pppm/stagger ` * :doc:`pppm/tip4p (o) ` * :doc:`pppm/dielectric ` - * :doc:`pppm/electrode ` * :doc:`pppm/electrode (i) ` * :doc:`scafacos ` diff --git a/doc/src/fix_electrode_conp.rst b/doc/src/fix_electrode_conp.rst index 45c0a56198..e936559b2e 100644 --- a/doc/src/fix_electrode_conp.rst +++ b/doc/src/fix_electrode_conp.rst @@ -8,20 +8,17 @@ fix electrode/conp command ========================== +Accelerator Variant: *electrode/conp/intel* + fix electrode/conq command ========================== +Accelerator Variant: *electrode/conq/intel* + fix electrode/thermo command ============================ -fix electrode/conp/intel command -================================ - -fix electrode/conq/intel command -================================ - -fix electrode/thermo/intel command -================================== +Accelerator Variant: *electrode/thermo/intel* Syntax """""" @@ -96,7 +93,7 @@ interactions. The Kspace styles *ewald/electrode*, *pppm/electrode* and For systems with non-periodic boundaries in one or two directions dipole corrections are available with the :doc:`kspace_modify `. For -ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` can be used +ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` can be used by setting "slab ew2d": .. code-block:: LAMMPS @@ -115,7 +112,7 @@ moderate mesh size but requires more memory. kspace_modify amat onestep/twostep -The *fix_modify tf* option allows to specify Thomas-Fermi parameters (:ref:`Scalfi `) for each atom type. +The *fix_modify tf* option allows to specify Thomas-Fermi parameters (:ref:`Scalfi `) for each atom type. .. code-block:: LAMMPS @@ -134,6 +131,10 @@ and top of the cell this can be achieved with *processors * * 2*. ---------- +.. include:: accel_styles.rst + +---------- + .. _Siepmann: **(Siepmann)** Siepmann and Strik, J. Chem. Phys. 102, 511 (1995). diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index c3e85ad88b..b1d6efa86c 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -56,7 +56,7 @@ Syntax *splittol* value = tol tol = relative size of two eigenvalues (see discussion below) *wire* value = volfactor (available with ELECTRODE package) - volfactor = ratio of the total extended dimension used in the 1d + volfactor = ratio of the total extended dimension used in the 1d approximation compared with the dimension of the simulation domain Examples diff --git a/examples/electrode/check_amat/.gitignore b/examples/PACKAGES/electrode/check_amat/.gitignore similarity index 100% rename from examples/electrode/check_amat/.gitignore rename to examples/PACKAGES/electrode/check_amat/.gitignore diff --git a/examples/electrode/check_amat/charged.data b/examples/PACKAGES/electrode/check_amat/charged.data similarity index 100% rename from examples/electrode/check_amat/charged.data rename to examples/PACKAGES/electrode/check_amat/charged.data diff --git a/examples/electrode/check_amat/charged.settings b/examples/PACKAGES/electrode/check_amat/charged.settings similarity index 100% rename from examples/electrode/check_amat/charged.settings rename to examples/PACKAGES/electrode/check_amat/charged.settings diff --git a/examples/electrode/check_amat/check.py b/examples/PACKAGES/electrode/check_amat/check.py similarity index 100% rename from examples/electrode/check_amat/check.py rename to examples/PACKAGES/electrode/check_amat/check.py diff --git a/examples/electrode/check_amat/check.sh b/examples/PACKAGES/electrode/check_amat/check.sh similarity index 100% rename from examples/electrode/check_amat/check.sh rename to examples/PACKAGES/electrode/check_amat/check.sh diff --git a/examples/electrode/check_amat/onestep.in b/examples/PACKAGES/electrode/check_amat/onestep.in similarity index 100% rename from examples/electrode/check_amat/onestep.in rename to examples/PACKAGES/electrode/check_amat/onestep.in diff --git a/examples/electrode/check_amat/twostep.in b/examples/PACKAGES/electrode/check_amat/twostep.in similarity index 100% rename from examples/electrode/check_amat/twostep.in rename to examples/PACKAGES/electrode/check_amat/twostep.in diff --git a/examples/electrode/check_conq/.gitignore b/examples/PACKAGES/electrode/check_conq/.gitignore similarity index 100% rename from examples/electrode/check_conq/.gitignore rename to examples/PACKAGES/electrode/check_conq/.gitignore diff --git a/examples/electrode/check_conq/cap.data b/examples/PACKAGES/electrode/check_conq/cap.data similarity index 100% rename from examples/electrode/check_conq/cap.data rename to examples/PACKAGES/electrode/check_conq/cap.data diff --git a/examples/electrode/check_conq/cgil.settings b/examples/PACKAGES/electrode/check_conq/cgil.settings similarity index 100% rename from examples/electrode/check_conq/cgil.settings rename to examples/PACKAGES/electrode/check_conq/cgil.settings diff --git a/examples/electrode/check_conq/equal.in b/examples/PACKAGES/electrode/check_conq/equal.in similarity index 100% rename from examples/electrode/check_conq/equal.in rename to examples/PACKAGES/electrode/check_conq/equal.in diff --git a/examples/electrode/check_conq/equal_intvars.in b/examples/PACKAGES/electrode/check_conq/equal_intvars.in similarity index 100% rename from examples/electrode/check_conq/equal_intvars.in rename to examples/PACKAGES/electrode/check_conq/equal_intvars.in diff --git a/examples/electrode/check_conq/p3m3dc.settings b/examples/PACKAGES/electrode/check_conq/p3m3dc.settings similarity index 100% rename from examples/electrode/check_conq/p3m3dc.settings rename to examples/PACKAGES/electrode/check_conq/p3m3dc.settings diff --git a/examples/electrode/check_conq/ramp.in b/examples/PACKAGES/electrode/check_conq/ramp.in similarity index 100% rename from examples/electrode/check_conq/ramp.in rename to examples/PACKAGES/electrode/check_conq/ramp.in diff --git a/examples/electrode/check_equalstyle/.gitignore b/examples/PACKAGES/electrode/check_equalstyle/.gitignore similarity index 100% rename from examples/electrode/check_equalstyle/.gitignore rename to examples/PACKAGES/electrode/check_equalstyle/.gitignore diff --git a/examples/electrode/check_equalstyle/cap.data b/examples/PACKAGES/electrode/check_equalstyle/cap.data similarity index 100% rename from examples/electrode/check_equalstyle/cap.data rename to examples/PACKAGES/electrode/check_equalstyle/cap.data diff --git a/examples/electrode/check_equalstyle/cgil.settings b/examples/PACKAGES/electrode/check_equalstyle/cgil.settings similarity index 100% rename from examples/electrode/check_equalstyle/cgil.settings rename to examples/PACKAGES/electrode/check_equalstyle/cgil.settings diff --git a/examples/electrode/check_equalstyle/check.py b/examples/PACKAGES/electrode/check_equalstyle/check.py similarity index 100% rename from examples/electrode/check_equalstyle/check.py rename to examples/PACKAGES/electrode/check_equalstyle/check.py diff --git a/examples/electrode/check_equalstyle/check.sh b/examples/PACKAGES/electrode/check_equalstyle/check.sh similarity index 100% rename from examples/electrode/check_equalstyle/check.sh rename to examples/PACKAGES/electrode/check_equalstyle/check.sh diff --git a/examples/electrode/check_equalstyle/const.in b/examples/PACKAGES/electrode/check_equalstyle/const.in similarity index 100% rename from examples/electrode/check_equalstyle/const.in rename to examples/PACKAGES/electrode/check_equalstyle/const.in diff --git a/examples/electrode/check_equalstyle/equal.in b/examples/PACKAGES/electrode/check_equalstyle/equal.in similarity index 100% rename from examples/electrode/check_equalstyle/equal.in rename to examples/PACKAGES/electrode/check_equalstyle/equal.in diff --git a/examples/electrode/check_equalstyle/p3m3dc.settings b/examples/PACKAGES/electrode/check_equalstyle/p3m3dc.settings similarity index 100% rename from examples/electrode/check_equalstyle/p3m3dc.settings rename to examples/PACKAGES/electrode/check_equalstyle/p3m3dc.settings diff --git a/examples/electrode/check_equalstyle/ramp.in b/examples/PACKAGES/electrode/check_equalstyle/ramp.in similarity index 100% rename from examples/electrode/check_equalstyle/ramp.in rename to examples/PACKAGES/electrode/check_equalstyle/ramp.in diff --git a/examples/electrode/check_etypes/.gitignore b/examples/PACKAGES/electrode/check_etypes/.gitignore similarity index 100% rename from examples/electrode/check_etypes/.gitignore rename to examples/PACKAGES/electrode/check_etypes/.gitignore diff --git a/examples/electrode/check_etypes/cap.data b/examples/PACKAGES/electrode/check_etypes/cap.data similarity index 100% rename from examples/electrode/check_etypes/cap.data rename to examples/PACKAGES/electrode/check_etypes/cap.data diff --git a/examples/electrode/check_etypes/cgil.settings b/examples/PACKAGES/electrode/check_etypes/cgil.settings similarity index 100% rename from examples/electrode/check_etypes/cgil.settings rename to examples/PACKAGES/electrode/check_etypes/cgil.settings diff --git a/examples/electrode/check_etypes/check.py b/examples/PACKAGES/electrode/check_etypes/check.py similarity index 100% rename from examples/electrode/check_etypes/check.py rename to examples/PACKAGES/electrode/check_etypes/check.py diff --git a/examples/electrode/check_etypes/check.sh b/examples/PACKAGES/electrode/check_etypes/check.sh similarity index 100% rename from examples/electrode/check_etypes/check.sh rename to examples/PACKAGES/electrode/check_etypes/check.sh diff --git a/examples/electrode/check_etypes/etypes.in b/examples/PACKAGES/electrode/check_etypes/etypes.in similarity index 100% rename from examples/electrode/check_etypes/etypes.in rename to examples/PACKAGES/electrode/check_etypes/etypes.in diff --git a/examples/electrode/check_etypes/p3m3dc.settings b/examples/PACKAGES/electrode/check_etypes/p3m3dc.settings similarity index 100% rename from examples/electrode/check_etypes/p3m3dc.settings rename to examples/PACKAGES/electrode/check_etypes/p3m3dc.settings diff --git a/examples/electrode/check_etypes/ref.in b/examples/PACKAGES/electrode/check_etypes/ref.in similarity index 100% rename from examples/electrode/check_etypes/ref.in rename to examples/PACKAGES/electrode/check_etypes/ref.in diff --git a/examples/electrode/check_ffield/.gitignore b/examples/PACKAGES/electrode/check_ffield/.gitignore similarity index 100% rename from examples/electrode/check_ffield/.gitignore rename to examples/PACKAGES/electrode/check_ffield/.gitignore diff --git a/examples/electrode/check_ffield/cap.data b/examples/PACKAGES/electrode/check_ffield/cap.data similarity index 100% rename from examples/electrode/check_ffield/cap.data rename to examples/PACKAGES/electrode/check_ffield/cap.data diff --git a/examples/electrode/check_ffield/cgil.settings b/examples/PACKAGES/electrode/check_ffield/cgil.settings similarity index 100% rename from examples/electrode/check_ffield/cgil.settings rename to examples/PACKAGES/electrode/check_ffield/cgil.settings diff --git a/examples/electrode/check_ffield/check.py b/examples/PACKAGES/electrode/check_ffield/check.py similarity index 100% rename from examples/electrode/check_ffield/check.py rename to examples/PACKAGES/electrode/check_ffield/check.py diff --git a/examples/electrode/check_ffield/check.sh b/examples/PACKAGES/electrode/check_ffield/check.sh similarity index 100% rename from examples/electrode/check_ffield/check.sh rename to examples/PACKAGES/electrode/check_ffield/check.sh diff --git a/examples/electrode/check_ffield/ffield.in b/examples/PACKAGES/electrode/check_ffield/ffield.in similarity index 100% rename from examples/electrode/check_ffield/ffield.in rename to examples/PACKAGES/electrode/check_ffield/ffield.in diff --git a/examples/electrode/check_ffield/ffield_flip.in b/examples/PACKAGES/electrode/check_ffield/ffield_flip.in similarity index 100% rename from examples/electrode/check_ffield/ffield_flip.in rename to examples/PACKAGES/electrode/check_ffield/ffield_flip.in diff --git a/examples/electrode/check_ffield/p3m.settings b/examples/PACKAGES/electrode/check_ffield/p3m.settings similarity index 100% rename from examples/electrode/check_ffield/p3m.settings rename to examples/PACKAGES/electrode/check_ffield/p3m.settings diff --git a/examples/electrode/check_ffield/p3m3dc.settings b/examples/PACKAGES/electrode/check_ffield/p3m3dc.settings similarity index 100% rename from examples/electrode/check_ffield/p3m3dc.settings rename to examples/PACKAGES/electrode/check_ffield/p3m3dc.settings diff --git a/examples/electrode/check_ffield/ref.in b/examples/PACKAGES/electrode/check_ffield/ref.in similarity index 100% rename from examples/electrode/check_ffield/ref.in rename to examples/PACKAGES/electrode/check_ffield/ref.in diff --git a/examples/electrode/check_hybrid/.gitignore b/examples/PACKAGES/electrode/check_hybrid/.gitignore similarity index 100% rename from examples/electrode/check_hybrid/.gitignore rename to examples/PACKAGES/electrode/check_hybrid/.gitignore diff --git a/examples/electrode/check_hybrid/cap.data b/examples/PACKAGES/electrode/check_hybrid/cap.data similarity index 100% rename from examples/electrode/check_hybrid/cap.data rename to examples/PACKAGES/electrode/check_hybrid/cap.data diff --git a/examples/electrode/check_hybrid/cgil.settings b/examples/PACKAGES/electrode/check_hybrid/cgil.settings similarity index 100% rename from examples/electrode/check_hybrid/cgil.settings rename to examples/PACKAGES/electrode/check_hybrid/cgil.settings diff --git a/examples/electrode/check_hybrid/coul.in b/examples/PACKAGES/electrode/check_hybrid/coul.in similarity index 100% rename from examples/electrode/check_hybrid/coul.in rename to examples/PACKAGES/electrode/check_hybrid/coul.in diff --git a/examples/electrode/check_hybrid/hybrid.in b/examples/PACKAGES/electrode/check_hybrid/hybrid.in similarity index 100% rename from examples/electrode/check_hybrid/hybrid.in rename to examples/PACKAGES/electrode/check_hybrid/hybrid.in diff --git a/examples/electrode/check_hybrid/lj.in b/examples/PACKAGES/electrode/check_hybrid/lj.in similarity index 100% rename from examples/electrode/check_hybrid/lj.in rename to examples/PACKAGES/electrode/check_hybrid/lj.in diff --git a/examples/electrode/check_hybrid/p3m3dc.settings b/examples/PACKAGES/electrode/check_hybrid/p3m3dc.settings similarity index 100% rename from examples/electrode/check_hybrid/p3m3dc.settings rename to examples/PACKAGES/electrode/check_hybrid/p3m3dc.settings diff --git a/examples/electrode/check_hybrid/ref.in b/examples/PACKAGES/electrode/check_hybrid/ref.in similarity index 100% rename from examples/electrode/check_hybrid/ref.in rename to examples/PACKAGES/electrode/check_hybrid/ref.in diff --git a/examples/electrode/check_intel/.gitignore b/examples/PACKAGES/electrode/check_intel/.gitignore similarity index 100% rename from examples/electrode/check_intel/.gitignore rename to examples/PACKAGES/electrode/check_intel/.gitignore diff --git a/examples/electrode/check_intel/cap.data b/examples/PACKAGES/electrode/check_intel/cap.data similarity index 100% rename from examples/electrode/check_intel/cap.data rename to examples/PACKAGES/electrode/check_intel/cap.data diff --git a/examples/electrode/check_intel/cgil.settings b/examples/PACKAGES/electrode/check_intel/cgil.settings similarity index 100% rename from examples/electrode/check_intel/cgil.settings rename to examples/PACKAGES/electrode/check_intel/cgil.settings diff --git a/examples/electrode/check_intel/check.py b/examples/PACKAGES/electrode/check_intel/check.py similarity index 100% rename from examples/electrode/check_intel/check.py rename to examples/PACKAGES/electrode/check_intel/check.py diff --git a/examples/electrode/check_intel/check.sh b/examples/PACKAGES/electrode/check_intel/check.sh similarity index 100% rename from examples/electrode/check_intel/check.sh rename to examples/PACKAGES/electrode/check_intel/check.sh diff --git a/examples/electrode/check_intel/p3m3dc.settings b/examples/PACKAGES/electrode/check_intel/p3m3dc.settings similarity index 100% rename from examples/electrode/check_intel/p3m3dc.settings rename to examples/PACKAGES/electrode/check_intel/p3m3dc.settings diff --git a/examples/electrode/check_intel/ref.in b/examples/PACKAGES/electrode/check_intel/ref.in similarity index 100% rename from examples/electrode/check_intel/ref.in rename to examples/PACKAGES/electrode/check_intel/ref.in diff --git a/examples/electrode/example/cap.data b/examples/PACKAGES/electrode/example/cap.data similarity index 100% rename from examples/electrode/example/cap.data rename to examples/PACKAGES/electrode/example/cap.data diff --git a/examples/electrode/example/conp.in b/examples/PACKAGES/electrode/example/conp.in similarity index 100% rename from examples/electrode/example/conp.in rename to examples/PACKAGES/electrode/example/conp.in diff --git a/examples/electrode/example/ew2d.settings b/examples/PACKAGES/electrode/example/ew2d.settings similarity index 100% rename from examples/electrode/example/ew2d.settings rename to examples/PACKAGES/electrode/example/ew2d.settings diff --git a/examples/electrode/example/ew3dc.settings b/examples/PACKAGES/electrode/example/ew3dc.settings similarity index 100% rename from examples/electrode/example/ew3dc.settings rename to examples/PACKAGES/electrode/example/ew3dc.settings diff --git a/examples/electrode/example/mw.settings b/examples/PACKAGES/electrode/example/mw.settings similarity index 100% rename from examples/electrode/example/mw.settings rename to examples/PACKAGES/electrode/example/mw.settings diff --git a/examples/electrode/example/p3m3dc.settings b/examples/PACKAGES/electrode/example/p3m3dc.settings similarity index 100% rename from examples/electrode/example/p3m3dc.settings rename to examples/PACKAGES/electrode/example/p3m3dc.settings diff --git a/examples/electrode/test_cgil_2d3d/.gitignore b/examples/PACKAGES/electrode/test_cgil_2d3d/.gitignore similarity index 100% rename from examples/electrode/test_cgil_2d3d/.gitignore rename to examples/PACKAGES/electrode/test_cgil_2d3d/.gitignore diff --git a/examples/electrode/test_cgil_2d3d/cap.data b/examples/PACKAGES/electrode/test_cgil_2d3d/cap.data similarity index 100% rename from examples/electrode/test_cgil_2d3d/cap.data rename to examples/PACKAGES/electrode/test_cgil_2d3d/cap.data diff --git a/examples/electrode/test_cgil_2d3d/cgil.settings b/examples/PACKAGES/electrode/test_cgil_2d3d/cgil.settings similarity index 100% rename from examples/electrode/test_cgil_2d3d/cgil.settings rename to examples/PACKAGES/electrode/test_cgil_2d3d/cgil.settings diff --git a/examples/electrode/test_cgil_2d3d/conp.in b/examples/PACKAGES/electrode/test_cgil_2d3d/conp.in similarity index 100% rename from examples/electrode/test_cgil_2d3d/conp.in rename to examples/PACKAGES/electrode/test_cgil_2d3d/conp.in diff --git a/examples/electrode/test_cgil_2d3d/ew2d.settings b/examples/PACKAGES/electrode/test_cgil_2d3d/ew2d.settings similarity index 100% rename from examples/electrode/test_cgil_2d3d/ew2d.settings rename to examples/PACKAGES/electrode/test_cgil_2d3d/ew2d.settings diff --git a/examples/electrode/test_cgil_2d3d/ew3dc.settings b/examples/PACKAGES/electrode/test_cgil_2d3d/ew3dc.settings similarity index 100% rename from examples/electrode/test_cgil_2d3d/ew3dc.settings rename to examples/PACKAGES/electrode/test_cgil_2d3d/ew3dc.settings diff --git a/examples/electrode/test_cgil_2d3d/p3m3dc.settings b/examples/PACKAGES/electrode/test_cgil_2d3d/p3m3dc.settings similarity index 100% rename from examples/electrode/test_cgil_2d3d/p3m3dc.settings rename to examples/PACKAGES/electrode/test_cgil_2d3d/p3m3dc.settings diff --git a/examples/electrode/test_cgil_2d3d/runtests.sh b/examples/PACKAGES/electrode/test_cgil_2d3d/runtests.sh similarity index 100% rename from examples/electrode/test_cgil_2d3d/runtests.sh rename to examples/PACKAGES/electrode/test_cgil_2d3d/runtests.sh diff --git a/examples/electrode/thermo/.gitignore b/examples/PACKAGES/electrode/thermo/.gitignore similarity index 100% rename from examples/electrode/thermo/.gitignore rename to examples/PACKAGES/electrode/thermo/.gitignore diff --git a/examples/electrode/thermo/conp/control.inp b/examples/PACKAGES/electrode/thermo/conp/control.inp similarity index 100% rename from examples/electrode/thermo/conp/control.inp rename to examples/PACKAGES/electrode/thermo/conp/control.inp diff --git a/examples/electrode/thermo/flat/control.inp b/examples/PACKAGES/electrode/thermo/flat/control.inp similarity index 100% rename from examples/electrode/thermo/flat/control.inp rename to examples/PACKAGES/electrode/thermo/flat/control.inp diff --git a/examples/electrode/thermo/potential.inp b/examples/PACKAGES/electrode/thermo/potential.inp similarity index 100% rename from examples/electrode/thermo/potential.inp rename to examples/PACKAGES/electrode/thermo/potential.inp diff --git a/examples/electrode/thermo/rng.py b/examples/PACKAGES/electrode/thermo/rng.py similarity index 100% rename from examples/electrode/thermo/rng.py rename to examples/PACKAGES/electrode/thermo/rng.py diff --git a/examples/electrode/thermo/sample.inp b/examples/PACKAGES/electrode/thermo/sample.inp similarity index 100% rename from examples/electrode/thermo/sample.inp rename to examples/PACKAGES/electrode/thermo/sample.inp diff --git a/examples/electrode/thermo/thermo/control.inp b/examples/PACKAGES/electrode/thermo/thermo/control.inp similarity index 100% rename from examples/electrode/thermo/thermo/control.inp rename to examples/PACKAGES/electrode/thermo/thermo/control.inp diff --git a/examples/electrode/thoams-fermi/.gitignore b/examples/PACKAGES/electrode/thoams-fermi/.gitignore similarity index 100% rename from examples/electrode/thoams-fermi/.gitignore rename to examples/PACKAGES/electrode/thoams-fermi/.gitignore diff --git a/examples/electrode/thoams-fermi/charged.data b/examples/PACKAGES/electrode/thoams-fermi/charged.data similarity index 100% rename from examples/electrode/thoams-fermi/charged.data rename to examples/PACKAGES/electrode/thoams-fermi/charged.data diff --git a/examples/electrode/thoams-fermi/charged.settings b/examples/PACKAGES/electrode/thoams-fermi/charged.settings similarity index 100% rename from examples/electrode/thoams-fermi/charged.settings rename to examples/PACKAGES/electrode/thoams-fermi/charged.settings diff --git a/examples/electrode/thoams-fermi/tf.in b/examples/PACKAGES/electrode/thoams-fermi/tf.in similarity index 100% rename from examples/electrode/thoams-fermi/tf.in rename to examples/PACKAGES/electrode/thoams-fermi/tf.in diff --git a/lib/electrode/Install.py b/lib/electrode/Install.py new file mode 120000 index 0000000000..ffe709d44c --- /dev/null +++ b/lib/electrode/Install.py @@ -0,0 +1 @@ +../Install.py \ No newline at end of file diff --git a/lib/electrode/Makefile.lammps.empty b/lib/electrode/Makefile.lammps.empty new file mode 100644 index 0000000000..9988ce4beb --- /dev/null +++ b/lib/electrode/Makefile.lammps.empty @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +electrode_SYSINC = +electrode_SYSLIB = +electrode_SYSPATH = diff --git a/lib/electrode/Makefile.lammps.installed b/lib/electrode/Makefile.lammps.installed new file mode 100644 index 0000000000..9c190bb38a --- /dev/null +++ b/lib/electrode/Makefile.lammps.installed @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +electrode_SYSINC = +electrode_SYSLIB = -lblas -llapack +electrode_SYSPATH = diff --git a/lib/electrode/Makefile.lammps.linalg b/lib/electrode/Makefile.lammps.linalg new file mode 100644 index 0000000000..e82066110e --- /dev/null +++ b/lib/electrode/Makefile.lammps.linalg @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +electrode_SYSINC = +electrode_SYSLIB = -llinalg -lgfortran +electrode_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/electrode/Makefile.mpi b/lib/electrode/Makefile.mpi new file mode 100644 index 0000000000..9233578db7 --- /dev/null +++ b/lib/electrode/Makefile.mpi @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libelectrode.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the ELECTRODE library to build with +# the same MPI library that LAMMPS is built with + +CC = mpicxx +CCFLAGS = -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/lib/electrode/Makefile.serial b/lib/electrode/Makefile.serial new file mode 100644 index 0000000000..8bdd02bae3 --- /dev/null +++ b/lib/electrode/Makefile.serial @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libelectrode.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the ATC library to build with +# the same MPI library that LAMMPS is built with + +CC = g++ +CCFLAGS = -O3 -fPIC -I../../src/STUBS + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/src/ELECTRODE/Install.sh b/src/ELECTRODE/Install.sh index 0406a43ee4..65d0b404da 100755 --- a/src/ELECTRODE/Install.sh +++ b/src/ELECTRODE/Install.sh @@ -14,33 +14,54 @@ export LC_ALL # arg1 = file, arg2 = file it depends on action () { - if (test $mode = 0) then - rm -f ../$1 - elif (! cmp -s $1 ../$1) then - if (test -z "$2" || test -e ../$2) then - cp $1 .. - if (test $mode = 2) then - echo " updating src/$1" - fi + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi fi - elif (test -n "$2") then - if (test ! -e ../$2) then - rm -f ../$1 - fi - fi } # all package files with no dependencies for file in *.cpp *.h; do - test -f ${file} && action $file + test -f ${file} && action $file done if (test $1 = 1) then + if (test ! -e ../pppm.cpp) then + echo "Must install KSPACE package with ELECTRODE" + exit 1 + fi + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/electrode |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lelectrode |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(electrode_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(electrode_SYSLIB) |' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ + include ..\/..\/lib\/electrode\/Makefile.lammps + ' ../Makefile.package.settings + fi - if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*conp[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_LIB =[ \t]*|&-llinalg -L../../lib/linalg$(LIBOBJDIR) -lgfortran |' ../Makefile.package - fi +elif (test $1 = 0) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + fi fi diff --git a/src/ELECTRODE/boundary_correction.cpp b/src/ELECTRODE/boundary_correction.cpp index eed9f7011a..a22e4bb1e1 100644 --- a/src/ELECTRODE/boundary_correction.cpp +++ b/src/ELECTRODE/boundary_correction.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -17,14 +17,11 @@ #include "boundary_correction.h" -#include - #include "atom.h" #include "comm.h" #include "force.h" using namespace LAMMPS_NS; -using namespace std; // use EW3DC slab correction // @@ -52,24 +49,24 @@ void BoundaryCorrection::setup(double x, double y, double z, double g) g_ewald = g; } -vector BoundaryCorrection::gather_recvcounts(int n) +std::vector BoundaryCorrection::gather_recvcounts(int n) { int const nprocs = comm->nprocs; - vector recvcounts = vector(nprocs); + std::vector recvcounts = std::vector(nprocs); MPI_Allgather(&n, 1, MPI_INT, &recvcounts.front(), 1, MPI_INT, world); return recvcounts; } -vector BoundaryCorrection::gather_displs(vector recvcounts) +std::vector BoundaryCorrection::gather_displs(const std::vector &recvcounts) { int const nprocs = comm->nprocs; - vector displs = vector(nprocs); + std::vector displs = std::vector(nprocs); displs[0] = 0; for (int i = 1; i < nprocs; i++) displs[i] = displs[i - 1] + recvcounts[i - 1]; return displs; } -vector BoundaryCorrection::gather_jmat(bigint *imat) +std::vector BoundaryCorrection::gather_jmat(bigint *imat) { int nlocal = atom->nlocal; bigint ngroup = 0; @@ -78,16 +75,16 @@ vector BoundaryCorrection::gather_jmat(bigint *imat) if (imat[i] > -1) ngrouplocal++; MPI_Allreduce(&ngrouplocal, &ngroup, 1, MPI_INT, MPI_SUM, world); - vector jmat_local = vector(ngrouplocal); + std::vector jmat_local = std::vector(ngrouplocal); for (int i = 0, n = 0; i < nlocal; i++) { if (imat[i] < 0) continue; jmat_local[n++] = imat[i]; } // gather global matrix indexing - vector jmat = vector(ngroup); - vector recvcounts = gather_recvcounts(ngrouplocal); - vector displs = gather_displs(recvcounts); + std::vector jmat = std::vector(ngroup); + std::vector recvcounts = gather_recvcounts(ngrouplocal); + std::vector displs = gather_displs(recvcounts); MPI_Allgatherv(&jmat_local.front(), ngrouplocal, MPI_LMP_BIGINT, &jmat.front(), &recvcounts.front(), &displs.front(), MPI_LMP_BIGINT, world); return jmat; diff --git a/src/ELECTRODE/boundary_correction.h b/src/ELECTRODE/boundary_correction.h index c1e8ac633e..dc25db569b 100644 --- a/src/ELECTRODE/boundary_correction.h +++ b/src/ELECTRODE/boundary_correction.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -43,7 +43,7 @@ class BoundaryCorrection : protected Pointers { std::vector gather_jmat(bigint *); std::vector gather_recvcounts(int); - std::vector gather_displs(std::vector); + std::vector gather_displs(const std::vector &); }; } // namespace LAMMPS_NS #endif diff --git a/src/ELECTRODE/electrode_accel_interface.cpp b/src/ELECTRODE/electrode_accel_interface.cpp deleted file mode 100644 index 746eb1b3ef..0000000000 --- a/src/ELECTRODE/electrode_accel_interface.cpp +++ /dev/null @@ -1,20 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing authors: Ludwig Ahrens-Iwers (TUHH), Shern Tee (UQ), Robert Meißner (TUHH) -------------------------------------------------------------------------- */ - -#include "electrode_accel_interface.h" - -LAMMPS_NS::ElectrodeAccelInterface::~ElectrodeAccelInterface() {} diff --git a/src/ELECTRODE/electrode_accel_interface.h b/src/ELECTRODE/electrode_accel_interface.h index 75bf3055bf..0d848bbf20 100644 --- a/src/ELECTRODE/electrode_accel_interface.h +++ b/src/ELECTRODE/electrode_accel_interface.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -25,7 +25,7 @@ namespace LAMMPS_NS { class ElectrodeAccelInterface : protected Pointers { public: ElectrodeAccelInterface(class LAMMPS *lmp) : Pointers(lmp) {} - virtual ~ElectrodeAccelInterface(); + virtual ~ElectrodeAccelInterface() {} virtual void intel_find_fix() {} virtual void intel_pack_buffers() {} }; diff --git a/src/ELECTRODE/electrode_kspace.h b/src/ELECTRODE/electrode_kspace.h index 824db6f730..7bd380a327 100644 --- a/src/ELECTRODE/electrode_kspace.h +++ b/src/ELECTRODE/electrode_kspace.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ELECTRODE/electrode_matrix.cpp b/src/ELECTRODE/electrode_matrix.cpp index 3a598b04a2..5b5d57b7c8 100644 --- a/src/ELECTRODE/electrode_matrix.cpp +++ b/src/ELECTRODE/electrode_matrix.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "electrode_kspace.h" #include "error.h" #include "force.h" #include "group.h" @@ -51,7 +52,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) : /* ---------------------------------------------------------------------- */ -void ElectrodeMatrix::setup(std::map tag_ids, class Pair *fix_pair, +void ElectrodeMatrix::setup(const std::map &tag_ids, class Pair *fix_pair, class NeighList *fix_neighlist) { pair = fix_pair; @@ -64,9 +65,10 @@ void ElectrodeMatrix::setup(std::map tag_ids, class Pair *fix_pair, tag_to_iele = tag_ids; } + /* ---------------------------------------------------------------------- */ -void ElectrodeMatrix::setup_tf(std::map tf_types) +void ElectrodeMatrix::setup_tf(const std::map &tf_types) { tfflag = true; this->tf_types = tf_types; diff --git a/src/ELECTRODE/electrode_matrix.h b/src/ELECTRODE/electrode_matrix.h index 229c4958b5..83ef0c5937 100644 --- a/src/ELECTRODE/electrode_matrix.h +++ b/src/ELECTRODE/electrode_matrix.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -15,19 +15,18 @@ Contributing authors: Ludwig Ahrens-Iwers (TUHH), Shern Tee (UQ), Robert Meißner (TUHH) ------------------------------------------------------------------------- */ -#include - -#include "electrode_kspace.h" #include "pointers.h" +#include + namespace LAMMPS_NS { class ElectrodeMatrix : protected Pointers { public: ElectrodeMatrix(class LAMMPS *, int, double); ~ElectrodeMatrix() {} - void setup(std::map, class Pair *, class NeighList *); - void setup_tf(std::map); + void setup(const std::map &, class Pair *, class NeighList *); + void setup_tf(const std::map &); void compute_array(double **); int igroup; diff --git a/src/ELECTRODE/electrode_vector.cpp b/src/ELECTRODE/electrode_vector.cpp index 203ccdf02e..5dd78f9b26 100644 --- a/src/ELECTRODE/electrode_vector.cpp +++ b/src/ELECTRODE/electrode_vector.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -19,6 +19,7 @@ #include "atom.h" #include "comm.h" +#include "electrode_kspace.h" #include "error.h" #include "force.h" #include "group.h" @@ -72,7 +73,7 @@ ElectrodeVector::~ElectrodeVector() /* ---------------------------------------------------------------------- */ -void ElectrodeVector::setup(std::map tag_ids, class Pair *fix_pair, +void ElectrodeVector::setup(const std::map &tag_ids, class Pair *fix_pair, class NeighList *fix_neighlist) { pair = fix_pair; diff --git a/src/ELECTRODE/electrode_vector.h b/src/ELECTRODE/electrode_vector.h index 81bc48ad94..ae2cd15f28 100644 --- a/src/ELECTRODE/electrode_vector.h +++ b/src/ELECTRODE/electrode_vector.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -15,18 +15,17 @@ Contributing authors: Ludwig Ahrens-Iwers (TUHH), Shern Tee (UQ), Robert Meißner (TUHH) ------------------------------------------------------------------------- */ -#include - -#include "electrode_kspace.h" #include "pointers.h" +#include + namespace LAMMPS_NS { class ElectrodeVector : protected Pointers { public: ElectrodeVector(class LAMMPS *, int, double); ~ElectrodeVector(); - void setup(std::map, class Pair *, class NeighList *); + void setup(const std::map &, class Pair *, class NeighList *); void compute_vector(); double *vector; int igroup; diff --git a/src/ELECTRODE/ewald_electrode.cpp b/src/ELECTRODE/ewald_electrode.cpp index 52a5ee44ca..ce17aa0824 100644 --- a/src/ELECTRODE/ewald_electrode.cpp +++ b/src/ELECTRODE/ewald_electrode.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -17,9 +17,6 @@ #include "ewald_electrode.h" -#include -#include - #include "atom.h" #include "comm.h" #include "domain.h" @@ -33,9 +30,11 @@ #include "update.h" #include "wire_dipole.h" +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; #define SMALL 0.00001 @@ -59,7 +58,7 @@ EwaldElectrode::~EwaldElectrode() void EwaldElectrode::init() { - if (comm->me == 0) utils::logmesg(lmp, "Ewald initialization ...\n"); + if (comm->me == 0) utils::logmesg(lmp, "Ewald/electrode initialization ...\n"); // error check if (domain->triclinic) error->all(FLERR, "Cannot (yet) use Ewald with triclinic box "); diff --git a/src/ELECTRODE/ewald_electrode.h b/src/ELECTRODE/ewald_electrode.h index e2b83cfb62..43999f240a 100644 --- a/src/ELECTRODE/ewald_electrode.h +++ b/src/ELECTRODE/ewald_electrode.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -18,7 +18,7 @@ #ifdef KSPACE_CLASS // clang-format off -KSpaceStyle(ewald/electrode, EwaldElectrode) +KSpaceStyle(ewald/electrode, EwaldElectrode); // clang-format on #else @@ -28,7 +28,6 @@ KSpaceStyle(ewald/electrode, EwaldElectrode) #include "electrode_kspace.h" #include "ewald.h" -#include namespace LAMMPS_NS { @@ -63,7 +62,7 @@ class EwaldElectrode : public Ewald, public ElectrodeKSpace { #endif #endif - /* ERROR/WARNING messages: +/* ERROR/WARNING messages: E: Illegal ... command diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index dc72583e34..c743e805b0 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -17,11 +17,6 @@ #include "fix_electrode_conp.h" -#include -#include -#include -#include - #include "atom.h" #include "comm.h" #include "compute.h" @@ -43,6 +38,11 @@ #include "pointers.h" #include "variable.h" +#include +#include +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -899,7 +899,7 @@ double FixElectrodeConp::compute_vector(int i) /* ---------------------------------------------------------------------- */ -double FixElectrodeConp::potential_energy(int eflag, std::vector mpos) +double FixElectrodeConp::potential_energy(int eflag, const std::vector &mpos) { // corrections to energy due to potential psi double const qqrd2e = force->qqrd2e; diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index 989806822a..50a5b22e26 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -18,7 +18,7 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(electrode/conp, FixElectrodeConp) +FixStyle(electrode/conp, FixElectrodeConp); // clang-format on #else @@ -26,12 +26,12 @@ FixStyle(electrode/conp, FixElectrodeConp) #ifndef LMP_FIX_ELECTRODE_CONP_H #define LMP_FIX_ELECTRODE_CONP_H -#include -#include - #include "electrode_accel_interface.h" #include "fix.h" +#include +#include + namespace LAMMPS_NS { class FixElectrodeConp : public Fix { @@ -90,7 +90,7 @@ class FixElectrodeConp : public Fix { void symmetrize(); double gausscorr(int, bool); void update_charges(); - double potential_energy(int, std::vector); + double potential_energy(int, const std::vector &); double self_energy(int); std::vector local_to_matrix(); void write_to_file(FILE *, std::vector, std::vector>); diff --git a/src/ELECTRODE/fix_electrode_conq.cpp b/src/ELECTRODE/fix_electrode_conq.cpp index 2d8b35778e..fa6240816c 100644 --- a/src/ELECTRODE/fix_electrode_conq.cpp +++ b/src/ELECTRODE/fix_electrode_conq.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ELECTRODE/fix_electrode_conq.h b/src/ELECTRODE/fix_electrode_conq.h index 478f8dfb86..40019a9667 100644 --- a/src/ELECTRODE/fix_electrode_conq.h +++ b/src/ELECTRODE/fix_electrode_conq.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -18,7 +18,7 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(electrode/conq, FixElectrodeConq) +FixStyle(electrode/conq, FixElectrodeConq); // clang-format on #else @@ -26,7 +26,6 @@ FixStyle(electrode/conq, FixElectrodeConq) #ifndef LMP_FIX_ELECTRODE_CONQ_H #define LMP_FIX_ELECTRODE_CONQ_H -#include "fix.h" #include "fix_electrode_conp.h" namespace LAMMPS_NS { diff --git a/src/ELECTRODE/fix_electrode_thermo.cpp b/src/ELECTRODE/fix_electrode_thermo.cpp index fe414d5ed9..940739029e 100644 --- a/src/ELECTRODE/fix_electrode_thermo.cpp +++ b/src/ELECTRODE/fix_electrode_thermo.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -27,7 +27,6 @@ #include "variable.h" using namespace LAMMPS_NS; -using namespace std; #define NUM_GROUPS 2 #define SMALL 0.00001 diff --git a/src/ELECTRODE/fix_electrode_thermo.h b/src/ELECTRODE/fix_electrode_thermo.h index 2e9c728305..e451e77d0f 100644 --- a/src/ELECTRODE/fix_electrode_thermo.h +++ b/src/ELECTRODE/fix_electrode_thermo.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -18,7 +18,7 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(electrode/thermo, FixElectrodeThermo) +FixStyle(electrode/thermo, FixElectrodeThermo); // clang-format on #else @@ -26,7 +26,6 @@ FixStyle(electrode/thermo, FixElectrodeThermo) #ifndef LMP_FIX_ELECTRODE_THERMO_H #define LMP_FIX_ELECTRODE_THERMO_H -#include "fix.h" #include "fix_electrode_conp.h" namespace LAMMPS_NS { diff --git a/src/ELECTRODE/pppm_electrode.cpp b/src/ELECTRODE/pppm_electrode.cpp index 7ecdd870dc..d96a88f342 100644 --- a/src/ELECTRODE/pppm_electrode.cpp +++ b/src/ELECTRODE/pppm_electrode.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -17,13 +17,10 @@ #include "pppm_electrode.h" -#include -#include -#include - #include "angle.h" #include "atom.h" #include "bond.h" +#include "boundary_correction.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -40,10 +37,13 @@ #include "update.h" #include "wire_dipole.h" +#include +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; -using namespace std; #define MAXORDER 7 #define OFFSET 16384 @@ -666,7 +666,7 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix) compute(1, 0); // fft green's function k -> r - vector greens_real(nz_pppm * ny_pppm * nx_pppm, 0.); + std::vector greens_real(nz_pppm * ny_pppm * nx_pppm, 0.); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -705,7 +705,7 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix) /* ----------------------------------------------------------------------*/ -void PPPMElectrode::one_step_multiplication(bigint *imat, vector greens_real, +void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector &greens_real, double **x_ele, double **matrix, int const nmat) { // map green's function in real space from mesh to particle positions @@ -718,8 +718,8 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, vector greens_ double step1_time = MPI_Wtime(); // precalculate rho_1d for local electrode - vector>> rho1d_j(nlocal, - vector>(3, vector(order, 0))); + std::vector>> rho1d_j( + nlocal, std::vector>(3, std::vector(order, 0))); for (int j = 0; j < nlocal; j++) { int jpos = imat[j]; if (jpos < 0) continue; @@ -795,7 +795,7 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, vector greens_ /* ----------------------------------------------------------------------*/ -void PPPMElectrode::two_step_multiplication(bigint *imat, vector greens_real, +void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vector &greens_real, double **x_ele, double **matrix, int const nmat) { // map green's function in real space from mesh to particle positions @@ -808,7 +808,7 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, vector greens_ int ny_ele = nyhi_out - nylo_out + 1; // ny_pppm + order + 1; int nz_ele = nzhi_out - nzlo_out + 1; // nz_pppm + order + 1; int nxyz = nx_ele * ny_ele * nz_ele; - vector> gw(nmat, vector(nxyz, 0.)); + std::vector> gw(nmat, std::vector(nxyz, 0.)); // loops over weights of electrode atoms and weights of complete grid // (nx,ny,nz) = global coords of grid pt to "lower left" of charge @@ -971,7 +971,7 @@ void PPPMElectrode::allocate_peratom() peratom_allocate_flag = 1; memory->create3d_offset(v0_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, - "pppm:v0_brick"); + "pppm:v0_brick"); memory->create3d_offset(v1_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, "pppm:v1_brick"); memory->create3d_offset(v2_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, diff --git a/src/ELECTRODE/pppm_electrode.h b/src/ELECTRODE/pppm_electrode.h index f3c4a9a13f..e02ed8e604 100644 --- a/src/ELECTRODE/pppm_electrode.h +++ b/src/ELECTRODE/pppm_electrode.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -18,7 +18,7 @@ #ifdef KSPACE_CLASS // clang-format off -KSpaceStyle(pppm/electrode, PPPMElectrode) +KSpaceStyle(pppm/electrode, PPPMElectrode); // clang-format on #else @@ -26,10 +26,8 @@ KSpaceStyle(pppm/electrode, PPPMElectrode) #ifndef LMP_PPPM_ELECTRODE_H #define LMP_PPPM_ELECTRODE_H -#include "boundary_correction.h" #include "electrode_kspace.h" #include "pppm.h" -#include #if defined(FFT_FFTW3) #define LMP_FFT_LIB "FFTW3" @@ -117,8 +115,10 @@ class PPPMElectrode : public PPPM, public ElectrodeKSpace { void start_compute(); void make_rho_in_brick(bigint *, FFT_SCALAR ***, bool); void project_psi(bigint *, double *vec); - void one_step_multiplication(bigint *, std::vector, double **, double **, int const); - void two_step_multiplication(bigint *, std::vector, double **, double **, int const); + void one_step_multiplication(bigint *, const std::vector &, double **, double **, + int const); + void two_step_multiplication(bigint *, const std::vector &, double **, double **, + int const); bool compute_vector_called; bigint *imat_cached; }; @@ -128,7 +128,7 @@ class PPPMElectrode : public PPPM, public ElectrodeKSpace { #endif #endif - /* ERROR/WARNING messages: +/* ERROR/WARNING messages: E: Illegal ... command diff --git a/src/ELECTRODE/slab_2d.cpp b/src/ELECTRODE/slab_2d.cpp index 249a37d2b7..373b3456df 100644 --- a/src/ELECTRODE/slab_2d.cpp +++ b/src/ELECTRODE/slab_2d.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -25,7 +25,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; /* ---------------------------------------------------------------------- Slab-geometry correction term (k=0) of EW2D. See Hu, JCTC 10:12 (2014) @@ -42,12 +41,12 @@ void Slab2d::compute_corr(double /*qsum*/, int eflag_atom, int eflag_global, dou int nlocal = atom->nlocal; bigint natoms = atom->natoms; - vector z = vector(nlocal); + std::vector z = std::vector(nlocal); for (int i = 0; i < nlocal; i++) z[i] = x[i][2]; - vector z_all = vector(natoms); - vector q_all = vector(natoms); - vector recvcounts = gather_recvcounts(nlocal); - vector displs = gather_displs(recvcounts); + std::vector z_all = std::vector(natoms); + std::vector q_all = std::vector(natoms); + std::vector recvcounts = gather_recvcounts(nlocal); + std::vector displs = gather_displs(recvcounts); MPI_Allgatherv(q, nlocal, MPI_DOUBLE, &q_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); MPI_Allgatherv(&z.front(), nlocal, MPI_DOUBLE, &z_all.front(), &recvcounts.front(), @@ -85,8 +84,8 @@ void Slab2d::vector_corr(bigint *imat, double *vec) int const nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q; - vector z_local; // z coordinates of electrolyte atoms - vector q_local; // charges of electrolyte atoms + std::vector z_local; // z coordinates of electrolyte atoms + std::vector q_local; // charges of electrolyte atoms for (int i = 0; i < nlocal; i++) { if (imat[i] < 0) { z_local.push_back(x[i][2]); @@ -97,10 +96,10 @@ void Slab2d::vector_corr(bigint *imat, double *vec) int n_electrolyte_local = z_local.size(); int n_electrolyte; MPI_Allreduce(&n_electrolyte_local, &n_electrolyte, 1, MPI_INT, MPI_SUM, world); - vector z_all = vector(n_electrolyte); - vector q_all = vector(n_electrolyte); - vector recvcounts = gather_recvcounts(n_electrolyte_local); - vector displs = gather_displs(recvcounts); + std::vector z_all = std::vector(n_electrolyte); + std::vector q_all = std::vector(n_electrolyte); + std::vector recvcounts = gather_recvcounts(n_electrolyte_local); + std::vector displs = gather_displs(recvcounts); MPI_Allgatherv(&z_local.front(), n_electrolyte_local, MPI_DOUBLE, &z_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); MPI_Allgatherv(&q_local.front(), n_electrolyte_local, MPI_DOUBLE, &q_all.front(), @@ -133,23 +132,23 @@ void Slab2d::matrix_corr(bigint *imat, double **matrix) MPI_Allreduce(&ngrouplocal, &ngroup, 1, MPI_INT, MPI_SUM, world); // gather non-periodic positions of groups - vector nprd_local = vector(ngrouplocal); + std::vector nprd_local = std::vector(ngrouplocal); for (int i = 0, n = 0; i < nlocal; i++) { if (imat[i] < 0) continue; nprd_local[n++] = x[i][2]; } // gather subsets nprd positions - vector recvcounts = gather_recvcounts(ngrouplocal); - vector displs = gather_displs(recvcounts); - vector nprd_all = vector(ngroup); + std::vector recvcounts = gather_recvcounts(ngrouplocal); + std::vector displs = gather_displs(recvcounts); + std::vector nprd_all = std::vector(ngroup); MPI_Allgatherv(&nprd_local.front(), ngrouplocal, MPI_DOUBLE, &nprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); const double g_ewald_inv = 1.0 / g_ewald; const double g_ewald_sq = g_ewald * g_ewald; const double prefac = 2.0 * MY_PIS / area; - vector jmat = gather_jmat(imat); + std::vector jmat = gather_jmat(imat); for (int i = 0; i < nlocal; i++) { if (imat[i] < 0) continue; for (bigint j = 0; j < ngroup; j++) { diff --git a/src/ELECTRODE/slab_2d.h b/src/ELECTRODE/slab_2d.h index 86913ef140..68718cbe37 100644 --- a/src/ELECTRODE/slab_2d.h +++ b/src/ELECTRODE/slab_2d.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ELECTRODE/slab_dipole.cpp b/src/ELECTRODE/slab_dipole.cpp index 612fbccf17..376f1e25d6 100644 --- a/src/ELECTRODE/slab_dipole.cpp +++ b/src/ELECTRODE/slab_dipole.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -24,7 +24,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; #define SMALL 0.00001 @@ -114,20 +113,20 @@ void SlabDipole::matrix_corr(bigint *imat, double **matrix) bigint ngroup = 0; MPI_Allreduce(&ngrouplocal, &ngroup, 1, MPI_INT, MPI_SUM, world); - vector nprd_local = vector(ngrouplocal); + std::vector nprd_local = std::vector(ngrouplocal); for (int i = 0, n = 0; i < nlocal; i++) { if (imat[i] < 0) continue; nprd_local[n++] = x[i][2]; } // gather subsets nprd positions - vector recvcounts = gather_recvcounts(ngrouplocal); - vector displs = gather_displs(recvcounts); - vector nprd_all = vector(ngroup); + std::vector recvcounts = gather_recvcounts(ngrouplocal); + std::vector displs = gather_displs(recvcounts); + std::vector nprd_all = std::vector(ngroup); MPI_Allgatherv(&nprd_local.front(), ngrouplocal, MPI_DOUBLE, &nprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); - vector jmat = gather_jmat(imat); + std::vector jmat = gather_jmat(imat); const double prefac = MY_4PI / volume; for (int i = 0; i < nlocal; i++) { if (imat[i] < 0) continue; diff --git a/src/ELECTRODE/slab_dipole.h b/src/ELECTRODE/slab_dipole.h index 2d3f566222..63c9f94828 100644 --- a/src/ELECTRODE/slab_dipole.h +++ b/src/ELECTRODE/slab_dipole.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ELECTRODE/wire_dipole.cpp b/src/ELECTRODE/wire_dipole.cpp index a1038858a8..94c5801abb 100644 --- a/src/ELECTRODE/wire_dipole.cpp +++ b/src/ELECTRODE/wire_dipole.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -24,7 +24,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; /* ---------------------------------------------------------------------- Wire-geometry correction term to dampen inter-wire interactions between @@ -125,8 +124,8 @@ void WireDipole::matrix_corr(bigint *imat, double **matrix) MPI_Allreduce(&ngrouplocal, &ngroup, 1, MPI_INT, MPI_SUM, world); // gather non-periodic positions of groups - vector xprd_local = vector(ngrouplocal); - vector yprd_local = vector(ngrouplocal); + std::vector xprd_local = std::vector(ngrouplocal); + std::vector yprd_local = std::vector(ngrouplocal); for (int i = 0, n = 0; i < nlocal; i++) { if (imat[i] < 0) continue; xprd_local[n] = x[i][0]; @@ -135,16 +134,16 @@ void WireDipole::matrix_corr(bigint *imat, double **matrix) } // gather subsets nprd positions - vector recvcounts = gather_recvcounts(ngrouplocal); - vector displs = gather_displs(recvcounts); - vector xprd_all = vector(ngroup); - vector yprd_all = vector(ngroup); + std::vector recvcounts = gather_recvcounts(ngrouplocal); + std::vector displs = gather_displs(recvcounts); + std::vector xprd_all = std::vector(ngroup); + std::vector yprd_all = std::vector(ngroup); MPI_Allgatherv(&xprd_local.front(), ngrouplocal, MPI_DOUBLE, &xprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); MPI_Allgatherv(&yprd_local.front(), ngrouplocal, MPI_DOUBLE, &yprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); - vector jmat = gather_jmat(imat); + std::vector jmat = gather_jmat(imat); const double prefac = MY_2PI / volume; for (int i = 0; i < nlocal; i++) { if (imat[i] < 0) continue; diff --git a/src/ELECTRODE/wire_dipole.h b/src/ELECTRODE/wire_dipole.h index 811fafc529..a30b97996b 100644 --- a/src/ELECTRODE/wire_dipole.h +++ b/src/ELECTRODE/wire_dipole.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/electrode_accel_intel.cpp b/src/INTEL/electrode_accel_intel.cpp index b21e834cd9..6f46452eef 100644 --- a/src/INTEL/electrode_accel_intel.cpp +++ b/src/INTEL/electrode_accel_intel.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/electrode_accel_intel.h b/src/INTEL/electrode_accel_intel.h index 5d236b9b34..7ef34b912b 100644 --- a/src/INTEL/electrode_accel_intel.h +++ b/src/INTEL/electrode_accel_intel.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/fix_electrode_conp_intel.h b/src/INTEL/fix_electrode_conp_intel.h index b1f0779984..0130fb2c55 100644 --- a/src/INTEL/fix_electrode_conp_intel.h +++ b/src/INTEL/fix_electrode_conp_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/fix_electrode_conq_intel.h b/src/INTEL/fix_electrode_conq_intel.h index ad9cc2ce40..5c5c166851 100644 --- a/src/INTEL/fix_electrode_conq_intel.h +++ b/src/INTEL/fix_electrode_conq_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/fix_electrode_thermo_intel.h b/src/INTEL/fix_electrode_thermo_intel.h index 5b56f35f1f..0625281972 100644 --- a/src/INTEL/fix_electrode_thermo_intel.h +++ b/src/INTEL/fix_electrode_thermo_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/pppm_electrode_intel.cpp b/src/INTEL/pppm_electrode_intel.cpp index ee065ae603..92b9728ea6 100644 --- a/src/INTEL/pppm_electrode_intel.cpp +++ b/src/INTEL/pppm_electrode_intel.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/pppm_electrode_intel.h b/src/INTEL/pppm_electrode_intel.h index b26035e112..33fdf35ef7 100644 --- a/src/INTEL/pppm_electrode_intel.h +++ b/src/INTEL/pppm_electrode_intel.h @@ -1,6 +1,6 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp index 9307ffd162..1e73fb940a 100644 --- a/src/INTEL/pppm_intel.cpp +++ b/src/INTEL/pppm_intel.cpp @@ -1159,12 +1159,12 @@ int PPPMIntel::use_base() { /* ---------------------------------------------------------------------- allows usage in derived classes (pppm/electrode/intel) ------------------------------------------------------------------------- */ -template void PPPMIntel::particle_map(IntelBuffers *buffers); +template void PPPMIntel::particle_map(IntelBuffers *buffers); template void PPPMIntel::particle_map(IntelBuffers *buffers); template void PPPMIntel::particle_map(IntelBuffers *buffers); -template void PPPMIntel::make_rho(IntelBuffers *buffers); +template void PPPMIntel::make_rho(IntelBuffers *buffers); template void PPPMIntel::make_rho(IntelBuffers *buffers); template void PPPMIntel::make_rho(IntelBuffers *buffers); -template void PPPMIntel::make_rho(IntelBuffers *buffers); +template void PPPMIntel::make_rho(IntelBuffers *buffers); template void PPPMIntel::make_rho(IntelBuffers *buffers); template void PPPMIntel::make_rho(IntelBuffers *buffers);