From da88305f4df4d6b4fec7c4570867cf80e61d3ccc Mon Sep 17 00:00:00 2001 From: jrgissing Date: Fri, 16 Nov 2018 20:41:49 -0700 Subject: [PATCH 1/3] bond/react: doc corrections, mostly formatting --- doc/src/fix_bond_react.txt | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 55a5785f7f..c0f60d84a0 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -25,7 +25,7 @@ common_keyword = {stabilization} :l {no} = no reaction site stabilization {yes} = perform reaction site stabilization {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 + {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 considered for the reaction :l @@ -36,13 +36,13 @@ react = mandatory argument indicating new reaction specification :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l - individual_keyword = {prob} or {stabilize_steps} :l + individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l {prob} values = fraction seed 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 fix :pre - {update_edges} value = {none} or {charges} :l + timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms + {update_edges} value = {none} or {charges} or {custom} none = do not update topology near the edges of reaction templates charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges :pre @@ -95,7 +95,7 @@ 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 -in an internally created fix "nve/limit"_fix_nve_limit.html time +in an internally-created fix "nve/limit"_fix_nve_limit.html time integrator for a set number of timesteps given by the {stabilize_steps} keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being @@ -122,12 +122,13 @@ 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 +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: +The following comments pertain to each {react} argument (in other +words, can be customized for each specified reaction): A check for possible new reaction sites is performed every {Nevery} timesteps. @@ -202,9 +203,9 @@ A discussion of correctly handling this is also provided on the The map file is a text document with the following format: A map file has a header and a body. The header of map file the -contains one mandatory keyword and two optional keywords. The mandatory -keyword is 'equivalences' and the optional keywords are 'edgeIDs' and -'customIDs': +contains one mandatory keyword and two optional keywords. The +mandatory keyword is 'equivalences' and the optional keywords are +'edgeIDs' and 'customIDs': N {equivalences} = # of atoms N in the reaction molecule templates N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template @@ -286,6 +287,14 @@ The {stabilize_steps} keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat. +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + The {update_edges} keyword can increase the number of atoms whose atomic charges are updated, when the pre-reaction template contains edge atoms. When the value is set to 'charges,' all atoms' atomic @@ -298,14 +307,6 @@ atom ID with a value of 'charges' will force the update of the atom's charge, even if it is near a template edge. Atoms not near a template edge are unaffected by this setting. -In order to produce the most physical behavior, this 'reaction site -equilibration time' should be tuned to be as small as possible while -retaining stability for a given system or reaction step. After a -limited number of case studies, this number has been set to a default -of 60 timesteps. Ideally, it should be individually tuned for each fix -reaction step. Note that in some situations, decreasing rather than -increasing this parameter will result in an increase in stability. - A few other considerations: It may be beneficial to ensure reacting atoms are at a certain From d7abb8cf4dda5b5df6f510a32fed7f2a437c509e Mon Sep 17 00:00:00 2001 From: jrgissing Date: Fri, 16 Nov 2018 20:42:52 -0700 Subject: [PATCH 2/3] Revert "bond/react: doc corrections, mostly formatting" This reverts commit da88305f4df4d6b4fec7c4570867cf80e61d3ccc. --- doc/src/fix_bond_react.txt | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index c0f60d84a0..55a5785f7f 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -25,7 +25,7 @@ common_keyword = {stabilization} :l {no} = no reaction site stabilization {yes} = perform reaction site stabilization {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 + {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 considered for the reaction :l @@ -36,13 +36,13 @@ react = mandatory argument indicating new reaction specification :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l - individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l + individual_keyword = {prob} or {stabilize_steps} :l {prob} values = fraction seed 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 the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms - {update_edges} value = {none} or {charges} or {custom} + timesteps = number of timesteps to apply internally created nve/limit fix :pre + {update_edges} value = {none} or {charges} :l none = do not update topology near the edges of reaction templates charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges :pre @@ -95,7 +95,7 @@ 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 -in an internally-created fix "nve/limit"_fix_nve_limit.html time +in an internally created fix "nve/limit"_fix_nve_limit.html time integrator for a set number of timesteps given by the {stabilize_steps} keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being @@ -122,13 +122,12 @@ 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 +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 (in other -words, can be customized for each specified reaction): +The following comments pertain to each {react} argument: A check for possible new reaction sites is performed every {Nevery} timesteps. @@ -203,9 +202,9 @@ A discussion of correctly handling this is also provided on the The map file is a text document with the following format: A map file has a header and a body. The header of map file the -contains one mandatory keyword and two optional keywords. The -mandatory keyword is 'equivalences' and the optional keywords are -'edgeIDs' and 'customIDs': +contains one mandatory keyword and two optional keywords. The mandatory +keyword is 'equivalences' and the optional keywords are 'edgeIDs' and +'customIDs': N {equivalences} = # of atoms N in the reaction molecule templates N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template @@ -287,14 +286,6 @@ The {stabilize_steps} keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat. -In order to produce the most physical behavior, this 'reaction site -equilibration time' should be tuned to be as small as possible while -retaining stability for a given system or reaction step. After a -limited number of case studies, this number has been set to a default -of 60 timesteps. Ideally, it should be individually tuned for each fix -reaction step. Note that in some situations, decreasing rather than -increasing this parameter will result in an increase in stability. - The {update_edges} keyword can increase the number of atoms whose atomic charges are updated, when the pre-reaction template contains edge atoms. When the value is set to 'charges,' all atoms' atomic @@ -307,6 +298,14 @@ atom ID with a value of 'charges' will force the update of the atom's charge, even if it is near a template edge. Atoms not near a template edge are unaffected by this setting. +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + A few other considerations: It may be beneficial to ensure reacting atoms are at a certain From 1d4e1f142572f70dacd6c66a1c1d0168ae720903 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Fri, 16 Nov 2018 20:47:51 -0700 Subject: [PATCH 3/3] bond/react:doc corrections --- doc/src/fix_bond_react.txt | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 55a5785f7f..ab7b247aaa 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -25,7 +25,7 @@ common_keyword = {stabilization} :l {no} = no reaction site stabilization {yes} = perform reaction site stabilization {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 + {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 considered for the reaction :l @@ -36,13 +36,13 @@ react = mandatory argument indicating new reaction specification :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l - individual_keyword = {prob} or {stabilize_steps} :l + individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l {prob} values = fraction seed 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 fix :pre - {update_edges} value = {none} or {charges} :l + timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms + {update_edges} value = {none} or {charges} or {custom} none = do not update topology near the edges of reaction templates charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges :pre @@ -95,7 +95,7 @@ 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 -in an internally created fix "nve/limit"_fix_nve_limit.html time +in an internally-created fix "nve/limit"_fix_nve_limit.html time integrator for a set number of timesteps given by the {stabilize_steps} keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being @@ -122,12 +122,13 @@ 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 +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: +The following comments pertain to each {react} argument (in other +words, can be customized for each reaction, or reaction step): A check for possible new reaction sites is performed every {Nevery} timesteps. @@ -202,9 +203,9 @@ A discussion of correctly handling this is also provided on the The map file is a text document with the following format: A map file has a header and a body. The header of map file the -contains one mandatory keyword and two optional keywords. The mandatory -keyword is 'equivalences' and the optional keywords are 'edgeIDs' and -'customIDs': +contains one mandatory keyword and two optional keywords. The +mandatory keyword is 'equivalences' and the optional keywords are +'edgeIDs' and 'customIDs': N {equivalences} = # of atoms N in the reaction molecule templates N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template @@ -286,6 +287,14 @@ The {stabilize_steps} keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat. +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + The {update_edges} keyword can increase the number of atoms whose atomic charges are updated, when the pre-reaction template contains edge atoms. When the value is set to 'charges,' all atoms' atomic @@ -298,14 +307,6 @@ atom ID with a value of 'charges' will force the update of the atom's charge, even if it is near a template edge. Atoms not near a template edge are unaffected by this setting. -In order to produce the most physical behavior, this 'reaction site -equilibration time' should be tuned to be as small as possible while -retaining stability for a given system or reaction step. After a -limited number of case studies, this number has been set to a default -of 60 timesteps. Ideally, it should be individually tuned for each fix -reaction step. Note that in some situations, decreasing rather than -increasing this parameter will result in an increase in stability. - A few other considerations: It may be beneficial to ensure reacting atoms are at a certain