diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index adc0eceda9..6c9a128447 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -132,14 +132,14 @@ at the cutoff distance :math:`r_c`. ---------- -Pair style *srp/react* interfaces the pair style *srp* with the -bond breaking and formation mechanisms provided by fix *bond/break* -and fix *bond/create*, respectively. When using this pair style, whenever a -bond breaking (or formation) reaction occurs, the corresponding fictitious -particle is deleted (or inserted) during the same simulation time step as -the reaction. This is useful in the simulation of reactive systems involving -large polymeric molecules :ref:`(Palkar) ` where the segmental repulsive -potential is necessary to minimize topological violations, and also needs to be +Pair style *srp/react* interfaces the pair style *srp* with the +bond breaking and formation mechanisms provided by fix *bond/break* +and fix *bond/create*, respectively. When using this pair style, whenever a +bond breaking (or formation) reaction occurs, the corresponding fictitious +particle is deleted (or inserted) during the same simulation time step as +the reaction. This is useful in the simulation of reactive systems involving +large polymeric molecules :ref:`(Palkar) ` where the segmental repulsive +potential is necessary to minimize topological violations, and also needs to be turned on and off according to the progress of the reaction. ---------- @@ -204,5 +204,5 @@ Chem Phys, 136 (13) 134903, 2012. .. _Palkar: -**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 +**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 diff --git a/src/MISC/fix_srp_react.cpp b/src/MISC/fix_srp_react.cpp index 2e12cd82b7..f4e790927d 100644 --- a/src/MISC/fix_srp_react.cpp +++ b/src/MISC/fix_srp_react.cpp @@ -13,13 +13,13 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) based on the pair srp code by Timothy Sirk (ARL) This pair style interfaces the pair style srp with the stochastic reaction fixes bond/break and bond/create by updating pseudo beads corresponding to bonds as bond breaking and formation takes place. This is useful in -simulation of reactions in polymers with soft potentials such as DPD. +simulation of reactions in polymers with soft potentials such as DPD. See the doc page for pair_style srp/react command for usage instructions. @@ -110,7 +110,7 @@ void FixSRPREACT::init() // find fix bond break if( idbreak != nullptr ) f_bb = (FixBondBreak *) modify->get_fix_by_id(idbreak); - + // find fix bond create if( idcreate != nullptr ) f_bc = (FixBondCreate *) modify->get_fix_by_id(idcreate); @@ -136,7 +136,7 @@ void FixSRPREACT::post_neighbor() //reset break count before exiting // not reseting breakcount would lead to redundant rebuilds f_bb->breakcount=0; - + // count additional call during setup_pre_force neighbor->ncalls = ncalls+1; } @@ -148,7 +148,7 @@ void FixSRPREACT::post_neighbor() //reset create count before exiting // not reseting createcount would lead to redundant rebuilds f_bc->createcount=0; - + // count additional call during setup_pre_force neighbor->ncalls = ncalls+1; } @@ -156,7 +156,7 @@ void FixSRPREACT::post_neighbor() /* ---------------------------------------------------------------------- interface with pair class - in addition to bond type and bond particle type, + in addition to bond type and bond particle type, pair srp react sets id of either fix bond break or bond create ------------------------------------------------------------------------- */ diff --git a/src/MISC/fix_srp_react.h b/src/MISC/fix_srp_react.h index 1b48c64385..8b583db6af 100644 --- a/src/MISC/fix_srp_react.h +++ b/src/MISC/fix_srp_react.h @@ -44,7 +44,3 @@ class FixSRPREACT : public FixSRP { #endif #endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index 46e058bad2..4f0720d27b 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -13,13 +13,13 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) based on the pair srp code by Timothy Sirk (ARL) This pair style interfaces the pair style srp with the stochastic reaction fixes bond/break and bond/create by updating pseudo beads corresponding to bonds as bond breaking and formation takes place. This is useful in -simulation of reactions in polymers with soft potentials such as DPD. +simulation of reactions in polymers with soft potentials such as DPD. See the doc page for pair_style srp/react command for usage instructions. @@ -213,7 +213,7 @@ void PairSRPREACT::init_style() f_srp->modify_params(2, arg0); delete [] idbreak; } - + // if using fix bond/create, set id of fix bond/create in fix srp // idcreate = id of fix bond break if( bond_create ) diff --git a/src/MISC/pair_srp_react.h b/src/MISC/pair_srp_react.h index 86e2c68111..39663996b0 100644 --- a/src/MISC/pair_srp_react.h +++ b/src/MISC/pair_srp_react.h @@ -40,7 +40,3 @@ class PairSRPREACT : public PairSRP { #endif #endif - -/* ERROR/WARNING messages: - -*/