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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
	examples/USER/openmp/parm.pegc12e8
	examples/USER/openmp/parm.pegc12e8-omp
This commit is contained in:
Axel Kohlmeyer
2014-04-09 13:49:45 +02:00
parent fb3a956155 51f4c3b0cc
commit f8daecd639
10 changed files with 47 additions and 95 deletions
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4
doc/Manual.html
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@ -1,7 +1,7 @@
<HTML> <HTML>
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Apr 2014 version"> <META NAME="docnumber" CONTENT="8 Apr 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation <CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER> </H3></CENTER>
<CENTER><H4>5 Apr 2014 version <CENTER><H4>8 Apr 2014 version
</H4></CENTER> </H4></CENTER>
<H4>Version info: <H4>Version info:
</H4> </H4>

4
doc/Manual.txt
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@ -1,7 +1,7 @@
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Apr 2014 version"> <META NAME="docnumber" CONTENT="8 Apr 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -19,7 +19,7 @@
<H1></H1> <H1></H1>
LAMMPS-ICMS Documentation :c,h3 LAMMPS-ICMS Documentation :c,h3
5 Apr 2014 version :c,h4 8 Apr 2014 version :c,h4
Version info: :h4 Version info: :h4

42
examples/USER/openmp/parm.pegc12e8
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@ -1,42 +0,0 @@
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0

42
examples/USER/openmp/parm.pegc12e8-omp
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@ -1,42 +0,0 @@
# Solvated 5-mer peptide CG force field
pair_style cg/cmm/omp 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0

6
src/MC/fix_bond_create.cpp
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@ -446,10 +446,12 @@ void FixBondCreate::post_integrate()
// increment bondcount, convert atom to new type if limit reached // increment bondcount, convert atom to new type if limit reached
bondcount[i]++; bondcount[i]++;
if (type[i] == iatomtype) int oldtype = type[i];
if (type[i] == iatomtype) {
if (bondcount[i] == imaxbond) type[i] = inewtype; if (bondcount[i] == imaxbond) type[i] = inewtype;
else } else {
if (bondcount[i] == jmaxbond) type[i] = jnewtype; if (bondcount[i] == jmaxbond) type[i] = jnewtype;
}
// count the created bond once // count the created bond once

32
src/MISC/fix_deposit.cpp
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@ -720,3 +720,35 @@ void FixDeposit::restart(char *buf)
random->reset(seed); random->reset(seed);
} }
/* ----------------------------------------------------------------------
extract particle radius for atom type = itype
------------------------------------------------------------------------- */
void *FixDeposit::extract(const char *str, int &itype)
{
if (strcmp(str,"radius") == 0) {
if (mode == ATOM) {
if (itype == ntype) oneradius = 0.5;
else oneradius = 0.0;
} else {
double *radius = onemol->radius;
int *type = onemol->type;
int natoms = onemol->natoms;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
}
}
itype = 0;
return &oneradius;
}
return NULL;
}

6
src/MISC/fix_deposit.h
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@ -27,8 +27,6 @@ namespace LAMMPS_NS {
class FixDeposit : public Fix { class FixDeposit : public Fix {
public: public:
int ntype; // type of deposited atom, visible to PairGran
FixDeposit(class LAMMPS *, int, char **); FixDeposit(class LAMMPS *, int, char **);
~FixDeposit(); ~FixDeposit();
int setmask(); int setmask();
@ -36,9 +34,10 @@ class FixDeposit : public Fix {
void pre_exchange(); void pre_exchange();
void write_restart(FILE *); void write_restart(FILE *);
void restart(char *); void restart(char *);
void *extract(const char *, int &);
private: private:
int ninsert,nfreq,seed; int ninsert,ntype,nfreq,seed;
int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag; int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
int mode,rigidflag,shakeflag,idnext; int mode,rigidflag,shakeflag,idnext;
double lo,hi,deltasq,nearsq,rate; double lo,hi,deltasq,nearsq,rate;
@ -53,6 +52,7 @@ class FixDeposit : public Fix {
double **coords; double **coords;
imageint *imageflags; imageint *imageflags;
class Fix *fixrigid,*fixshake; class Fix *fixrigid,*fixshake;
double oneradius;
int nfirst,ninserted; int nfirst,ninserted;
tagint maxtag_all,maxmol_all; tagint maxtag_all,maxmol_all;

3
src/atom.cpp
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@ -162,7 +162,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
tag_enable = 1; tag_enable = 1;
map_style = map_user = 0; map_style = map_user = 0;
map_tag_max = -1; map_tag_max = -1;
map_maxarray = map_nhash = 0; map_maxarray = map_nhash = -1;
max_same = 0; max_same = 0;
sametag = NULL; sametag = NULL;
@ -480,6 +480,7 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"array") == 0) map_user = 1; if (strcmp(arg[iarg+1],"array") == 0) map_user = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2; else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2;
else error->all(FLERR,"Illegal atom_modify command"); else error->all(FLERR,"Illegal atom_modify command");
map_style = map_user;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) { } else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command"); if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");

1
src/atom_map.cpp
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@ -37,6 +37,7 @@ void Atom::map_init(int check)
// check for new map style if max atomID changed (check = 1 = default) // check for new map style if max atomID changed (check = 1 = default)
// recreate = 1 if must delete old map and create new map // recreate = 1 if must delete old map and create new map
// recreate = 0 if can re-use old map w/out realloc and just adjust settings // recreate = 0 if can re-use old map w/out realloc and just adjust settings
// map_maxarray/map_nhash initially -1, to force recreate even when no atoms
int recreate = 0; int recreate = 0;
if (check) recreate = map_style_set(); if (check) recreate = map_style_set();

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "5 Apr 2014" #define LAMMPS_VERSION "8 Apr 2014"