Loading doc/src/fix_bond_break.txt +2 −2 Original line number Diff line number Diff line Loading @@ -137,8 +137,8 @@ doc page for more info. [Related commands:] "fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] Loading doc/src/fix_bond_create.txt +2 −2 Original line number Diff line number Diff line Loading @@ -232,8 +232,8 @@ doc page for more info. [Related commands:] "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] Loading doc/src/fix_bond_react.txt +27 −17 Original line number Diff line number Diff line Loading @@ -24,11 +24,11 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization {group-ID} = user-assigned ID for all non-reacting atoms (group created internally) {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l react-group-ID = only atoms in this group are available for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l Nevery = attempt reaction every this many steps :l Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l Loading @@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :l molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre molecule mol1 pre_reacted_rxn1.txt molecule mol2 post_reacted_rxn1.txt Loading @@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.txt fix 5 all bond/react stabilization yes nvt_grp .03 & react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre [Description:] Loading Loading @@ -102,19 +102,29 @@ involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation. The group-ID set using the {stabilization} keyword should be a previously unused group-ID. It cannot be specified as 'all'. The fix bond/react command creates a "dynamic group"_group.html of this name that includes all non-reacting atoms. This dynamic group-ID should then be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. It is currently necessary to place the time integration command after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: The internally created group currently applies to all atoms in the system, i.e. you should generally not have a separate thermostat which acts on the 'all' group. The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, the fix bond/react command creates a "dynamic group"_group.html that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is used as the parent group of new, internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group contains only non-reacting atoms at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. NOTE: If the group-ID is previously unused, the internally created group applies to all atoms in the system, i.e. you should generally not have a separate thermostat which acts on the 'all' group, or any other group. The following comments pertain to each {react} argument: Loading doc/src/fix_nve_dot.txt +4 −2 Original line number Diff line number Diff line Loading @@ -36,8 +36,8 @@ The command is equivalent to the "fix nve"_fix_nve.html. The particles are always considered to have a finite size. An example input file can be found in /examples/USER/cgdna/examples/duplex1/. A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -59,3 +59,5 @@ See the "Build package"_Build_package.html doc page for more info. [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). :link(Miller1) [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). :link(Henrich3) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). doc/src/fix_nve_dotc_langevin.txt +4 −2 Original line number Diff line number Diff line Loading @@ -114,8 +114,8 @@ The scale factor after the {angmom} keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -139,3 +139,5 @@ See the "Build package"_Build_package.html doc page for more info. [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). :link(Dunweg3) [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991). :link(Henrich4) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). Loading
doc/src/fix_bond_break.txt +2 −2 Original line number Diff line number Diff line Loading @@ -137,8 +137,8 @@ doc page for more info. [Related commands:] "fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] Loading
doc/src/fix_bond_create.txt +2 −2 Original line number Diff line number Diff line Loading @@ -232,8 +232,8 @@ doc page for more info. [Related commands:] "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] Loading
doc/src/fix_bond_react.txt +27 −17 Original line number Diff line number Diff line Loading @@ -24,11 +24,11 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization {group-ID} = user-assigned ID for all non-reacting atoms (group created internally) {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l react-group-ID = only atoms in this group are available for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l Nevery = attempt reaction every this many steps :l Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l Loading @@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :l molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre molecule mol1 pre_reacted_rxn1.txt molecule mol2 post_reacted_rxn1.txt Loading @@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.txt fix 5 all bond/react stabilization yes nvt_grp .03 & react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre [Description:] Loading Loading @@ -102,19 +102,29 @@ involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation. The group-ID set using the {stabilization} keyword should be a previously unused group-ID. It cannot be specified as 'all'. The fix bond/react command creates a "dynamic group"_group.html of this name that includes all non-reacting atoms. This dynamic group-ID should then be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. It is currently necessary to place the time integration command after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: The internally created group currently applies to all atoms in the system, i.e. you should generally not have a separate thermostat which acts on the 'all' group. The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, the fix bond/react command creates a "dynamic group"_group.html that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is used as the parent group of new, internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group contains only non-reacting atoms at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. NOTE: If the group-ID is previously unused, the internally created group applies to all atoms in the system, i.e. you should generally not have a separate thermostat which acts on the 'all' group, or any other group. The following comments pertain to each {react} argument: Loading
doc/src/fix_nve_dot.txt +4 −2 Original line number Diff line number Diff line Loading @@ -36,8 +36,8 @@ The command is equivalent to the "fix nve"_fix_nve.html. The particles are always considered to have a finite size. An example input file can be found in /examples/USER/cgdna/examples/duplex1/. A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -59,3 +59,5 @@ See the "Build package"_Build_package.html doc page for more info. [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). :link(Miller1) [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). :link(Henrich3) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
doc/src/fix_nve_dotc_langevin.txt +4 −2 Original line number Diff line number Diff line Loading @@ -114,8 +114,8 @@ The scale factor after the {angmom} keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -139,3 +139,5 @@ See the "Build package"_Build_package.html doc page for more info. [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). :link(Dunweg3) [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991). :link(Henrich4) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
