fix code related issues (53ccc4c6) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -420,7 +420,7 @@ endforeach()
		##############################################
		# add lib sources of (simple) enabled packages
		############################################
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
		if(PKG_${SIMPLE_LIB})
		string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
		string(TOLOWER "${PKG_LIB}" PKG_LIB)

doc/src/Commands_compute.rst

+8 −8

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
		KOKKOS, o = USER-OMP, t = OPT.

		.. table_from_list::
		:columns: 5
		:columns: 6

		* :doc:`ackland/atom <compute_ackland_atom>`
		* :doc:`adf <compute_adf>`
		@@ -39,13 +39,6 @@ KOKKOS, o = USER-OMP, t = OPT.
		* :doc:`cluster/atom <compute_cluster_atom>`
		* :doc:`cna/atom <compute_cna_atom>`
		* :doc:`cnp/atom <compute_cnp_atom>`
		* :doc:`cnt/Es <compute_cnt>`
		* :doc:`cnt/Eb <compute_cnt>`
		* :doc:`cnt/Et <compute_cnt>`
		* :doc:`cnt/B <compute_cnt>`
		* :doc:`cnt/Es_tot <compute_cnt>`
		* :doc:`cnt/Eb_tot <compute_cnt>`
		* :doc:`cnt/Et_tot <compute_cnt>`
		* :doc:`com <compute_com>`
		* :doc:`com/chunk <compute_com_chunk>`
		* :doc:`contact/atom <compute_contact_atom>`
		@@ -86,6 +79,13 @@ KOKKOS, o = USER-OMP, t = OPT.
		* :doc:`ke/atom/eff <compute_ke_atom_eff>`
		* :doc:`ke/eff <compute_ke_eff>`
		* :doc:`ke/rigid <compute_ke_rigid>`
		* :doc:`mesont/Es <compute_mesont>`
		* :doc:`mesont/Eb <compute_mesont>`
		* :doc:`mesont/Et <compute_mesont>`
		* :doc:`mesont/B <compute_mesont>`
		* :doc:`mesont/Es_tot <compute_mesont>`
		* :doc:`mesont/Eb_tot <compute_mesont>`
		* :doc:`mesont/Et_tot <compute_mesont>`
		* :doc:`meso/e/atom <compute_meso_e_atom>`
		* :doc:`meso/rho/atom <compute_meso_rho_atom>`
		* :doc:`meso/t/atom <compute_meso_t_atom>`

doc/src/Commands_pair.rst

+3 −5

Original line number	Diff line number	Diff line
		@@ -26,10 +26,6 @@ OPT.
		* :doc:`zero <pair_zero>`
		* :doc:`hybrid (k) <pair_hybrid>`
		* :doc:`hybrid/overlay (k) <pair_hybrid>`
		* :doc:`kim <pair_kim>`
		* :doc:`list <pair_list>`
		*
		*
		*
		*
		*
		@@ -64,7 +60,6 @@ OPT.
		* :doc:`buck/mdf <pair_mdf>`
		* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
		* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
		* :doc:`cnt/tpm <pair_cnt_tpm>`
		* :doc:`colloid (go) <pair_colloid>`
		* :doc:`comb (o) <pair_comb>`
		* :doc:`comb3 <pair_comb>`
		@@ -113,12 +108,14 @@ OPT.
		* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
		* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
		* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
		* :doc:`kim <pair_kim>`
		* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
		* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
		* :doc:`lcbop <pair_lcbop>`
		* :doc:`lebedeva/z <pair_lebedeva_z>`
		* :doc:`lennard/mdf <pair_mdf>`
		* :doc:`line/lj <pair_line_lj>`
		* :doc:`list <pair_list>`
		* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
		* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
		* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
		@@ -178,6 +175,7 @@ OPT.
		* :doc:`meam/spline (o) <pair_meam_spline>`
		* :doc:`meam/sw/spline <pair_meam_sw_spline>`
		* :doc:`mesocnt <pair_mesocnt>`
		* :doc:`mesont/tpm <pair_mesont_tpm>`
		* :doc:`mgpt <pair_mgpt>`
		* :doc:`mie/cut (g) <pair_mie>`
		* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`

doc/src/Packages_details.rst

+39 −0

Original line number	Diff line number	Diff line
		@@ -82,6 +82,7 @@ page gives those details.
		* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
		* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
		* :ref:`USER-MESO <PKG-USER-MESO>`
		* :ref:`USER-MESONT <PKG-USER-MESONT>`
		* :ref:`USER-MGPT <PKG-USER-MGPT>`
		* :ref:`USER-MISC <PKG-USER-MISC>`
		* :ref:`USER-MOFFF <PKG-USER-MOFFF>`
		@@ -1826,6 +1827,44 @@ algorithm.
		----------


		.. _PKG-USER-MESONT:

		USER-MESONT package
		-------------------

		Contents:

		USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon
		nanotubes (NTs). The model is based on a coarse-grained representation
		of CNTs as "flexible cylinders" consisting of a variable number of
		segments. Internal interactions within a CNT and the van der Waals
		interaction between the tubes are described by a mesoscopic force
		field designed and parameterized based on the results of atomic-level
		molecular dynamics simulations. The description of the force field
		is provided in the papers listed below.

		Author: Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)

		Supporting info:

		* src/USER-MESONT: filenames -> commands
		* src/USER-MESONT/README
		* :doc:`atom_style mesont <atom_style>`
		* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
		* :doc:`mesont/Es <compute_mesont>`
		* :doc:`mesont/Eb <compute_mesont>`
		* :doc:`mesont/Et <compute_mesont>`
		* :doc:`mesont/B <compute_mesont>`
		* :doc:`mesont/Es_tot <compute_mesont>`
		* :doc:`mesont/Eb_tot <compute_mesont>`
		* :doc:`mesont/Et_tot <compute_mesont>`
		* examples/USER/mesont
		* tools/mesont


		----------


		.. _PKG-USER-MOFFF:

		USER-MOFFF package

doc/src/Packages_user.rst

+2 −0

Original line number	Diff line number	Diff line
		@@ -67,6 +67,8 @@ package:
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
		\| :ref:`USER-MESO <PKG-USER-MESO>` \| mesoscale DPD models \| :doc:`pair_style edpd <pair_meso>` \| USER/meso \| no \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
		\| :ref:`USER-MESONT <PKG-USER-MESONT>` \| mesoscopic tubular potential model \| :doc:`pair_style mesont/tpm <pair_mesont_tpm>` \| USER/mesont \| int \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
		\| :ref:`USER-MGPT <PKG-USER-MGPT>` \| fast MGPT multi-ion potentials \| :doc:`pair_style mgpt <pair_mgpt>` \| USER/mgpt \| no \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
		\| :ref:`USER-MISC <PKG-USER-MISC>` \| single-file contributions \| USER-MISC/README \| USER/misc \| no \|

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