Loading doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -683,6 +683,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, "bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, Loading doc/src/fix_bond_react.txt +16 −15 Original line number Diff line number Diff line Loading @@ -39,7 +39,7 @@ react = mandatory argument indicating new reaction specification fraction = initiate reaction with this probability if otherwise eligible seed = random number seed (positive integer) {stabilize_steps} value = timesteps timesteps = number of timesteps to apply internally created nve/limit :pre timesteps = number of timesteps to apply internally created nve/limit.html :pre :ule [Examples:] Loading Loading @@ -85,7 +85,7 @@ with fix/bond react. Only one 'fix bond/react' command can be used at a time. Multiple reactions can be simultaneously applied by specifying multiple 'react' arguments to a single 'fix bond/react' command. This syntax is necessary because the ‘common keywords’ are applied to all reactions. necessary because the 'common keywords' are applied to all reactions. The {stabilization} keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms Loading Loading @@ -178,7 +178,7 @@ description of the file. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only whitespace after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn’t contain a header keyword, the line begins the body of the doesn't contain a header keyword, the line begins the body of the file. The header contains one mandatory keyword and one optional keyword. Loading @@ -203,8 +203,7 @@ order. The value(s) are read from the beginning of the line. Thus the keyword 'equivalences' should be in a line like "25 equivalences." equivalences = # of atoms in the pre- and post-reacted molecule templates edgeIDs = # of edge atoms in the pre-reacted molecule template templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre The edgeIDs keyword is optional. Loading @@ -228,21 +227,22 @@ pre-reacted molecule template. A sample map file is given below: --------------- this is a map file :line # This is a map file :pre 2 edgeIDs 7 equivalences 7 equivalences :pre BondingIDs BondingIDs :pre 3 5 3 5 :pre EdgeIDs EdgeIDs :pre 1 7 1 7 :pre Equivalences Equivalences :pre 1 1 2 2 Loading @@ -250,8 +250,9 @@ Equivalences 4 4 5 5 6 6 7 7 --------------- 7 7 :pre :line Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the Loading doc/src/fixes.txt +1 −0 Original line number Diff line number Diff line Loading @@ -23,6 +23,7 @@ Fixes :h1 fix_bond_break fix_bond_create fix_bond_swap fix_bond_react fix_box_relax fix_cmap fix_colvars Loading doc/src/lammps.book +1 −0 Original line number Diff line number Diff line Loading @@ -150,6 +150,7 @@ fix_aveforce.html fix_balance.html fix_bond_break.html fix_bond_create.html fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html Loading Loading
doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -683,6 +683,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, "bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, Loading
doc/src/fix_bond_react.txt +16 −15 Original line number Diff line number Diff line Loading @@ -39,7 +39,7 @@ react = mandatory argument indicating new reaction specification fraction = initiate reaction with this probability if otherwise eligible seed = random number seed (positive integer) {stabilize_steps} value = timesteps timesteps = number of timesteps to apply internally created nve/limit :pre timesteps = number of timesteps to apply internally created nve/limit.html :pre :ule [Examples:] Loading Loading @@ -85,7 +85,7 @@ with fix/bond react. Only one 'fix bond/react' command can be used at a time. Multiple reactions can be simultaneously applied by specifying multiple 'react' arguments to a single 'fix bond/react' command. This syntax is necessary because the ‘common keywords’ are applied to all reactions. necessary because the 'common keywords' are applied to all reactions. The {stabilization} keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms Loading Loading @@ -178,7 +178,7 @@ description of the file. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only whitespace after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn’t contain a header keyword, the line begins the body of the doesn't contain a header keyword, the line begins the body of the file. The header contains one mandatory keyword and one optional keyword. Loading @@ -203,8 +203,7 @@ order. The value(s) are read from the beginning of the line. Thus the keyword 'equivalences' should be in a line like "25 equivalences." equivalences = # of atoms in the pre- and post-reacted molecule templates edgeIDs = # of edge atoms in the pre-reacted molecule template templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre The edgeIDs keyword is optional. Loading @@ -228,21 +227,22 @@ pre-reacted molecule template. A sample map file is given below: --------------- this is a map file :line # This is a map file :pre 2 edgeIDs 7 equivalences 7 equivalences :pre BondingIDs BondingIDs :pre 3 5 3 5 :pre EdgeIDs EdgeIDs :pre 1 7 1 7 :pre Equivalences Equivalences :pre 1 1 2 2 Loading @@ -250,8 +250,9 @@ Equivalences 4 4 5 5 6 6 7 7 --------------- 7 7 :pre :line Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the Loading
doc/src/fixes.txt +1 −0 Original line number Diff line number Diff line Loading @@ -23,6 +23,7 @@ Fixes :h1 fix_bond_break fix_bond_create fix_bond_swap fix_bond_react fix_box_relax fix_cmap fix_colvars Loading
doc/src/lammps.book +1 −0 Original line number Diff line number Diff line Loading @@ -150,6 +150,7 @@ fix_aveforce.html fix_balance.html fix_bond_break.html fix_bond_create.html fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html Loading
