Loading doc/src/Errors_messages.rst +3 −0 Original line number Diff line number Diff line Loading @@ -489,6 +489,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` Only systems with bonds that can be changed can be used. Atom\_style template does not qualify. *Bond/react: Invalid template atom ID in map file* Atom IDs in molecule templates range from 1 to the number of atoms in the template. *Bond/react: Rmax cutoff is longer than pairwise cutoff* This is not allowed because bond creation is done using the pairwise neighbor list. Loading doc/src/Howto_bash.rst +2 −2 Original line number Diff line number Diff line Loading @@ -115,8 +115,8 @@ Files in Ubuntu on Windows ^^^^^^^^^^^^^^^^^^^^^^^^^^ When you launch "Bash on Ubuntu on Windows" you will start out in your Linux user home directory /home/\ **username**\ . You can access your Windows user directory using the /mnt/c/Users/\ **username** folder. user home directory /home/[username]\ . You can access your Windows user directory using the /mnt/c/Users/[username] folder. Download LAMMPS ^^^^^^^^^^^^^^^ Loading doc/src/compute_angle_local.rst +4 −4 Original line number Diff line number Diff line Loading @@ -81,12 +81,12 @@ and output the statistics in various ways: compute 1 all property/local aatom1 aatom2 aatom3 atype compute 2 all angle/local eng theta v_cos v_cossq set theta t dump 1 all local 100 tmp.dump c_1**\*** c_2**\*** dump 1 all local 100 tmp.dump c_1[*] c_2[*] compute 3 all reduce ave c_2**\*** thermo_style custom step temp press c_3**\*** compute 3 all reduce ave c_2[*] thermo_style custom step temp press c_3[*] fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **3** mode vector file tmp.histo fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo The :doc:`dump local <dump>` command will output the energy, angle, cosine(angle), cosine\^2(angle) for every angle in the system. The Loading doc/src/compute_bond_local.rst +4 −4 Original line number Diff line number Diff line Loading @@ -134,12 +134,12 @@ output the statistics in various ways: compute 1 all property/local batom1 batom2 btype compute 2 all bond/local engpot dist v_dsq set dist d dump 1 all local 100 tmp.dump c_1**\*** c_2**\*** dump 1 all local 100 tmp.dump c_1[*] c_2[*] compute 3 all reduce ave c_2**\*** thermo_style custom step temp press c_3**\*** compute 3 all reduce ave c_2[*] thermo_style custom step temp press c_3[*] fix 10 all ave/histo 10 10 100 0 6 20 c_2\ **3** mode vector file tmp.histo fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo The :doc:`dump local <dump>` command will output the energy, distance, distance\^2 for every bond in the system. The Loading doc/src/compute_chunk_spread_atom.rst +4 −4 Original line number Diff line number Diff line Loading @@ -32,7 +32,7 @@ Examples .. parsed-literal:: compute 1 all chunk/spread/atom mychunk c_com**\*** c_gyration compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration Description """"""""""" Loading Loading @@ -109,7 +109,7 @@ with 3 columns: .. parsed-literal:: compute com all com/chunk mychunk compute 10 all chunk/spread/atom mychunk c_com[\*] compute 10 all chunk/spread/atom mychunk c_com[*] compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3] Loading @@ -125,8 +125,8 @@ to the bench/in.chain script. compute cmol all chunk/atom molecule compute com all com/chunk cmol compute comchunk all chunk/spread/atom cmol c_com**\*** dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk**\*** compute comchunk all chunk/spread/atom cmol c_com[*] dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*] dump_modify 1 sort id The same per-chunk data for each atom could be used to define per-atom Loading Loading
doc/src/Errors_messages.rst +3 −0 Original line number Diff line number Diff line Loading @@ -489,6 +489,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` Only systems with bonds that can be changed can be used. Atom\_style template does not qualify. *Bond/react: Invalid template atom ID in map file* Atom IDs in molecule templates range from 1 to the number of atoms in the template. *Bond/react: Rmax cutoff is longer than pairwise cutoff* This is not allowed because bond creation is done using the pairwise neighbor list. Loading
doc/src/Howto_bash.rst +2 −2 Original line number Diff line number Diff line Loading @@ -115,8 +115,8 @@ Files in Ubuntu on Windows ^^^^^^^^^^^^^^^^^^^^^^^^^^ When you launch "Bash on Ubuntu on Windows" you will start out in your Linux user home directory /home/\ **username**\ . You can access your Windows user directory using the /mnt/c/Users/\ **username** folder. user home directory /home/[username]\ . You can access your Windows user directory using the /mnt/c/Users/[username] folder. Download LAMMPS ^^^^^^^^^^^^^^^ Loading
doc/src/compute_angle_local.rst +4 −4 Original line number Diff line number Diff line Loading @@ -81,12 +81,12 @@ and output the statistics in various ways: compute 1 all property/local aatom1 aatom2 aatom3 atype compute 2 all angle/local eng theta v_cos v_cossq set theta t dump 1 all local 100 tmp.dump c_1**\*** c_2**\*** dump 1 all local 100 tmp.dump c_1[*] c_2[*] compute 3 all reduce ave c_2**\*** thermo_style custom step temp press c_3**\*** compute 3 all reduce ave c_2[*] thermo_style custom step temp press c_3[*] fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **3** mode vector file tmp.histo fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo The :doc:`dump local <dump>` command will output the energy, angle, cosine(angle), cosine\^2(angle) for every angle in the system. The Loading
doc/src/compute_bond_local.rst +4 −4 Original line number Diff line number Diff line Loading @@ -134,12 +134,12 @@ output the statistics in various ways: compute 1 all property/local batom1 batom2 btype compute 2 all bond/local engpot dist v_dsq set dist d dump 1 all local 100 tmp.dump c_1**\*** c_2**\*** dump 1 all local 100 tmp.dump c_1[*] c_2[*] compute 3 all reduce ave c_2**\*** thermo_style custom step temp press c_3**\*** compute 3 all reduce ave c_2[*] thermo_style custom step temp press c_3[*] fix 10 all ave/histo 10 10 100 0 6 20 c_2\ **3** mode vector file tmp.histo fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo The :doc:`dump local <dump>` command will output the energy, distance, distance\^2 for every bond in the system. The Loading
doc/src/compute_chunk_spread_atom.rst +4 −4 Original line number Diff line number Diff line Loading @@ -32,7 +32,7 @@ Examples .. parsed-literal:: compute 1 all chunk/spread/atom mychunk c_com**\*** c_gyration compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration Description """"""""""" Loading Loading @@ -109,7 +109,7 @@ with 3 columns: .. parsed-literal:: compute com all com/chunk mychunk compute 10 all chunk/spread/atom mychunk c_com[\*] compute 10 all chunk/spread/atom mychunk c_com[*] compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3] Loading @@ -125,8 +125,8 @@ to the bench/in.chain script. compute cmol all chunk/atom molecule compute com all com/chunk cmol compute comchunk all chunk/spread/atom cmol c_com**\*** dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk**\*** compute comchunk all chunk/spread/atom cmol c_com[*] dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*] dump_modify 1 sort id The same per-chunk data for each atom could be used to define per-atom Loading
