From 080fe0b70fb45eea7c70be838eb58ed8fc15f37e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 21 Nov 2014 16:34:34 +0000 Subject: [PATCH 1/3] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12765 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/atom.cpp b/src/atom.cpp index d328f0975f..9d494b35db 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -519,7 +519,7 @@ void Atom::modify_params(int narg, char **arg) else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 2; else error->all(FLERR,"Illegal atom_modify command"); iarg += 2; - } if (strcmp(arg[iarg],"map") == 0) { + } else if (strcmp(arg[iarg],"map") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command"); if (domain->box_exist) error->all(FLERR, From b90439226f6703eb5a4d9f1860abf209bb36b5b2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 22 Nov 2014 00:28:49 +0000 Subject: [PATCH 2/3] git-svn-id: 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(o)tip4p/long/soft (o) +srptersoff/table (o)tip4p/long/soft (o)
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 74b37daac8..f53ad4353a 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -846,6 +846,7 @@ package"_Section_start.html#start_3. "sph/rhosum"_pair_sph_rhosum.html, "sph/taitwater"_pair_sph_taitwater.html, "sph/taitwater/morris"_pair_sph_taitwater_morris.html, +"srp"_pair_srp.html, "tersoff/table (o)"_pair_tersoff.html, "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) diff --git a/doc/pair_srp.html b/doc/pair_srp.html new file mode 100644 index 0000000000..eb29965e24 --- /dev/null +++ b/doc/pair_srp.html @@ -0,0 +1,164 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

pair_style srp command +

+

Syntax: +

+

pair_style srp cutoff bond_type dist keyword value ... +

+
  • cutoff = global cutoff for SRP interactions (distance units) + +
  • bond_type = bond type to apply SRP interactions + +
  • dist = min or mid + +
  • zero or more keyword/value pairs may be appended + +
  • keyword = exclude + +
      exclude value = yes or no 
+
    + +
+

Examples: +

+
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
+pair_coeff 1 1 dpd 60.0 4.5 1.0 
+pair_coeff 1 2 none 
+pair_coeff 2 2 srp 100.0 0.8 
+
+
pair_style hybrid srp 0.8 1 mid exclude yes
+pair_coeff 1 1 none 
+pair_coeff 1 2 none 
+pair_coeff 2 2 srp 100.0 0.8 
+
+

Description: +

+

Style srp computes a soft segmental repulsive potential (SRP) that +acts between bonds. This potential is useful in preventing bonds from +passing through one another when a soft non-bonded potential acts +between beads in, for example, DPD polymer chains. +An example input script that uses this command is provided +in examples/USER/srp. +

+

Bonds of type btype interact with one another through a +bond-pairwise potential, such that the force on bond i due to bond +j is as follows +

+
+
+

where r and rij are the distance and unit vector between the two +bonds. The mid option computes r and rij from the midpoint +distance between bonds. The min option computes r and rij from +the minimum distance between bonds. The force acting on a bond is +mapped onto the two bond atoms according to the lever rule, +

+
+
+

where L is the normalized distance from the atom to the point of +closest approach of bond i and j. The mid option takes L as +0.5 for each interaction as described in (Sirk). +

+

The following coefficients must be defined via the +pair_coeff command as in the examples above, or in +the data file or restart file read by the read_data +or read_restart commands: +

+
  • C (force units) +
  • Rc (distance units) +
+

The last coefficient is optional. If not specified, the global cutoff +is used. +

+

IMPORTANT NOTE: Pair style srp considers each bond of type btype as +a fictitious particle of type bptype, where bptype is the largest +atom type in the system. These "bond particles" are inserted at the +beginning of the run, and serve as placeholders that define the +position of the bonds. This allows neighbor lists to be constructed +and pairwise interactions to be computed in almost the same way as is +done for point particles. Because bonds interact only with other +bonds, pair_style hybrid should be used to turn off +interactions between atom type bptype and all other types of atoms. +An error will be flagged if pair_style hybrid is +not used. Further, only bond particles should be given an atom type +of bptype; a check is done at the beginning of the run to ensure +there are no regular atoms of bptype. +

+

The optional exclude keyword determines if forces are computed +between first neighbor (directly connected) bonds. For a setting of +yes they are, for no they are not. +

+

Pair style srp turns off normalization of thermodynamic properties +by particle number, as if the command thermo_modify norm +no had been issued. A warning will be given if +this setting is overridden in the input script. +

+

The pairwise energy associated with style srp is shifted to be zero +at the cutoff distance Rc. +

+
+ +

Mixing, shift, table, tail correction, restart, rRESPA info: +

+

This pair styles does not support mixing. +

+

This pair style does not support the pair_modify +shift option for the energy of the pair interaction. Note that as +discussed above, the energy term is already shifted to be 0.0 at the +cutoff distance rc. +

+

The pair_modify table option is not relevant for +this pair style. +

+

This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +

+

This pair style writes global and per-atom information to binary +restart files. Pair srp should be used with pair_style +hybrid, thus the pair_coeff commands need to be +specified in the input script when reading a restart file. +

+

This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords. +

+
+ +

Restrictions: +

+

This pair style is part of the USER-MISC package. It is only enabled +if LAMMPS was built with that package. See the Making LAMMPS section +for more info. +

+

This pair style must be used with pair_style hybrid. +

+

This pair style requires the newton command to be on +for non-bonded interactions. +

+

Related commands: +

+

pair_style hybrid, pair_coeff, +pair dpd +

+

Default: +

+

The default keyword value is exclude = yes. +

+
+ + + +

(Sirk) Sirk TW, Slizoberg YR, Brennan JK, Lisal M, Andzelm JW, J +Chem Phys, 136 (13) 134903, 2012. +

+ diff --git a/doc/pair_srp.txt b/doc/pair_srp.txt new file mode 100644 index 0000000000..feaef1b59b --- /dev/null +++ b/doc/pair_srp.txt @@ -0,0 +1,152 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style srp command :h3 + +[Syntax:] + +pair_style srp cutoff bond_type dist keyword value ... + +cutoff = global cutoff for SRP interactions (distance units) :ulb,l +bond_type = bond type to apply SRP interactions :l +dist = {min} or {mid} :l +zero or more keyword/value pairs may be appended :l +keyword = {exclude} :l + {exclude} value = {yes} or {no} :pre +:ule + +[Examples:] + +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes +pair_coeff 1 1 dpd 60.0 4.5 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 :pre + +pair_style hybrid srp 0.8 1 mid exclude yes +pair_coeff 1 1 none +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 :pre + +[Description:] + +Style {srp} computes a soft segmental repulsive potential (SRP) that +acts between bonds. This potential is useful in preventing bonds from +passing through one another when a soft non-bonded potential acts +between beads in, for example, DPD polymer chains. +An example input script that uses this command is provided +in examples/USER/srp. + +Bonds of type {btype} interact with one another through a +bond-pairwise potential, such that the force on bond {i} due to bond +{j} is as follows + +:c,image(Eqs/pair_srp1.jpg) + +where {r} and {rij} are the distance and unit vector between the two +bonds. The {mid} option computes {r} and {rij} from the midpoint +distance between bonds. The {min} option computes {r} and {rij} from +the minimum distance between bonds. The force acting on a bond is +mapped onto the two bond atoms according to the lever rule, + +:c,image(Eqs/pair_srp2.jpg) + +where {L} is the normalized distance from the atom to the point of +closest approach of bond {i} and {j}. The {mid} option takes {L} as +0.5 for each interaction as described in "(Sirk)"_#Sirk. + +The following coefficients must be defined via the +"pair_coeff"_pair_coeff.html command as in the examples above, or in +the data file or restart file read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +{C} (force units) +{Rc} (distance units) :ul + +The last coefficient is optional. If not specified, the global cutoff +is used. + +IMPORTANT NOTE: Pair style srp considers each bond of type {btype} as +a fictitious particle of type {bptype}, where {bptype} is the largest +atom type in the system. These "bond particles" are inserted at the +beginning of the run, and serve as placeholders that define the +position of the bonds. This allows neighbor lists to be constructed +and pairwise interactions to be computed in almost the same way as is +done for point particles. Because bonds interact only with other +bonds, "pair_style hybrid"_pair_hybrid.html should be used to turn off +interactions between atom type {bptype} and all other types of atoms. +An error will be flagged if "pair_style hybrid"_pair_hybrid.html is +not used. Further, only bond particles should be given an atom type +of {bptype}; a check is done at the beginning of the run to ensure +there are no regular atoms of {bptype}. + +The optional {exclude} keyword determines if forces are computed +between first neighbor (directly connected) bonds. For a setting of +{yes} they are, for {no} they are not. + +Pair style {srp} turns off normalization of thermodynamic properties +by particle number, as if the command "thermo_modify norm +no"_thermo_modify.html had been issued. A warning will be given if +this setting is overridden in the input script. + +The pairwise energy associated with style {srp} is shifted to be zero +at the cutoff distance {Rc}. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair styles does not support mixing. + +This pair style does not support the "pair_modify"_pair_modify.html +shift option for the energy of the pair interaction. Note that as +discussed above, the energy term is already shifted to be 0.0 at the +cutoff distance {rc}. + +The "pair_modify"_pair_modify.html table option is not relevant for +this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style writes global and per-atom information to "binary +restart files"_restart.html. Pair srp should be used with "pair_style +hybrid"_pair_hybrid.html, thus the pair_coeff commands need to be +specified in the input script when reading a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style is part of the USER-MISC package. It is only enabled +if LAMMPS was built with that package. See the Making LAMMPS section +for more info. + +This pair style must be used with "pair_style hybrid"_pair_hybrid.html. + +This pair style requires the "newton"_newton.html command to be {on} +for non-bonded interactions. + +[Related commands:] + +"pair_style hybrid"_pair_hybrid.html, "pair_coeff"_pair_coeff.html, +"pair dpd"_pair_dpd.html + +[Default:] + +The default keyword value is exclude = yes. + +:line + +:link(Sirk) +[(Sirk)] Sirk TW, Slizoberg YR, Brennan JK, Lisal M, Andzelm JW, J +Chem Phys, 136 (13) 134903, 2012. From af1adefecfdc91aed3b008924a7d2aed8aaa4a62 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 22 Nov 2014 00:36:53 +0000 Subject: [PATCH 3/3] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12767 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/pair_dpd.html | 7 ++++++- doc/pair_dpd.txt | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index efc260dfd4..4fe2e5ab4f 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -103,6 +103,11 @@ except that A is not included.

The GPU-accelerated versions of these styles are implemented based on the work of (Afshar) and (Phillips).

+

IMPORTANT NOTE: If you are modeling DPD polymer chains, you may want +to use the pair_style srp command in conjuction with +these pair styles. It is a soft segmental repulsive potential (SRP) +that can prevent DPD polymer chains from crossing each other. +

Styles with a cuda, gpu, intel, kk, omp, or opt suffix are @@ -189,7 +194,7 @@ compute depend on atom velocities. See the

Related commands:

pair_coeff, fix nvt, fix -langevin +langevin, pair_style srp

Default: none

diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt index 00918ad713..1ebffdea2a 100644 --- a/doc/pair_dpd.txt +++ b/doc/pair_dpd.txt @@ -95,6 +95,11 @@ except that A is not included. The GPU-accelerated versions of these styles are implemented based on the work of "(Afshar)"_#Afshar and "(Phillips)"_#Phillips. +IMPORTANT NOTE: If you are modeling DPD polymer chains, you may want +to use the "pair_style srp"_pair_srp.html command in conjuction with +these pair styles. It is a soft segmental repulsive potential (SRP) +that can prevent DPD polymer chains from crossing each other. + :line Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -181,7 +186,7 @@ compute depend on atom velocities. See the [Related commands:] "pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix -langevin"_fix_langevin.html +langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html [Default:] none