[liggghts] 02/06: Merge.
Anton Gladky
gladk at moszumanska.debian.org
Tue Mar 17 21:41:29 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch experimental
in repository liggghts.
commit 708fb847c8e204042926ae5bb30b0b7a2f62ee94
Merge: 4d4603b 39f1279
Author: Anton Gladky <gladk at debian.org>
Date: Tue Mar 17 21:12:58 2015 +0100
Merge.
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tools/pymol_asphere/src/m_constants.h | 67 -
tools/pymol_asphere/src/make_manpages.sh | 24 -
tools/pymol_asphere/src/misc.cpp | 428 -
tools/pymol_asphere/src/misc.h | 165 -
tools/pymol_asphere/src/miscm.cpp | 212 -
tools/pymol_asphere/src/miscm.h | 89 -
tools/pymol_asphere/src/spherical.cpp | 147 -
tools/pymol_asphere/src/spherical.h | 113 -
tools/python/README | 113 -
tools/python/dump2cfg.py | 32 -
tools/python/dump2pdb.py | 37 -
tools/python/dump2xyz.py | 32 -
tools/python/dumpsort.py | 26 -
tools/python/log2txt.py | 32 -
tools/python/logplot.py | 28 -
tools/python/neb_combine.py | 88 -
tools/python/neb_final.py | 71 -
tools/python/pizza/cfg.py | 187 -
tools/python/pizza/dump.py | 1231 -
tools/python/pizza/gnu.py | 383 -
tools/python/pizza/log.py | 338 -
tools/python/pizza/pdbfile.py | 289 -
tools/python/pizza/xyz.py | 121 -
tools/reax/Cutoff.dic | 14 -
tools/reax/README.txt | 22 -
tools/reax/bondConnectCheck.f90 | 232 -
tools/reax/bonds.reax | 784 -
tools/reax/mol_fra.c | 801 -
tools/reax/reaxc_bond.pl | 152 -
tools/restart2data.cpp | 4227 -
tools/vim/README.txt | 54 -
tools/vim/lammps.vim | 63 -
tools/vim/mysyntax.vim | 4 -
tools/vim/vimrc | 2 -
tools/xmgrace/README | 16 -
tools/xmgrace/lammpsplot.cpp | 830 -
tools/xmgrace/lammpsplot.pdf | Bin 71715 -> 0 bytes
tools/xmgrace/logplotawk.oneliner | 7 -
tools/xmgrace/logplotgrep.oneliner | 6 -
tools/xmgrace/plotthermodata.awk | 18 -
tools/xmovie/Makefile | 63 -
tools/xmovie/README | 51 -
tools/xmovie/Xdefaults | 51 -
tools/xmovie/control.c | 1340 -
tools/xmovie/dummy.c | 63 -
tools/xmovie/dummy.dat | 8004 -
tools/xmovie/hpsort.c | 43 -
tools/xmovie/read.c | 1239 -
tools/xmovie/resource.h | 244 -
tools/xmovie/scene.c | 673 -
tools/xmovie/toascii.c | 425 -
tools/xmovie/tobinary.c | 525 -
tools/xmovie/version.c | 15 -
tools/xmovie/xmovie.c | 282 -
tools/xmovie/xmovie.h | 161 -
1321 files changed, 8498 insertions(+), 701576 deletions(-)
diff --cc src/container_base.cpp
index 969da4e,2613f2b..2c9fc1f
--- a/src/container_base.cpp
+++ b/src/container_base.cpp
@@@ -77,9 -69,9 +86,10 @@@ using namespace LAMMPS_NS
: id_(0),
communicationType_(COMM_TYPE_MANUAL),
refFrame_(REF_FRAME_UNDEFINED),
+>>>>>>> upstream/3.0.0
restartType_(RESTART_TYPE_UNDEFINED),
- scalePower_(-1)
+ scalePower_(-1),
+ useDefault_(false)
{
setProperties(_id, _comm, _ref,_restart,_scalePower);
}
diff --cc src/fix_cfd_coupling_force_implicit.cpp
index 8643e35,d6d6b2b..a1621e5
--- a/src/fix_cfd_coupling_force_implicit.cpp
+++ b/src/fix_cfd_coupling_force_implicit.cpp
@@@ -204,30 -195,9 +208,30 @@@ void FixCfdCouplingForceImplicit::post_
void FixCfdCouplingForceImplicit::end_of_step()
{
+<<<<<<< HEAD
+
+ if(!useCN_) return; //return if CN not used
+
+ double **x = atom->x;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *Ksl = fix_Ksl_->vector_atom;
+ double **uf = fix_uf_->array_atom;
+ double **dragforce = fix_dragforce_->array_atom;
+ double KslMDeltaT, deltaU;
+ double vN32[3];
+ double frc[3];
+
+=======
if(!useCN_) return; //return if CN not used
-
+
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
diff --cc src/fix_massflow_mesh.cpp
index 06b4e03,d786f76..882bfde
--- a/src/fix_massflow_mesh.cpp
+++ b/src/fix_massflow_mesh.cpp
@@@ -379,14 -412,19 +412,22 @@@ void FixMassflowMesh::post_integrate(
// particle is now on nvec_ side
if(dot > 0.)
{
- if(compDouble(counter[iPart],0.)) //particle was not on nvec_ side before
+ //particle was not on nvec_ side before
+ if((ibody > -1) ? ((*ms_counter_)(ibody) == 0) : (compDouble(counter[iPart],0.)) ) // compDouble(counter[iPart],0.))
{
+
mass_this += rmass[iPart];
nparticles_this ++;
+ if(fix_property_)
+ {
+
+ property_this += fix_property_->vector_atom[iPart];
+ }
+
if(delete_atoms_)
+<<<<<<< HEAD
+ atom_tags_delete_.push_back(atom->tag[iPart]);
+=======
{
atom_tags_delete_.push_back(atom->tag[iPart]);
}
diff --cc src/fix_mesh_surface_stress_servo.cpp
index bac0cd9,63be229..8dbb4e9
--- a/src/fix_mesh_surface_stress_servo.cpp
+++ b/src/fix_mesh_surface_stress_servo.cpp
@@@ -241,9 -157,8 +245,9 @@@ FixMeshSurfaceStressServo::FixMeshSurfa
if (sp_mag_ == 0.) error->fix_error(FLERR,this,"'target_val' (desired force/torque) has to be != 0.0");
sp_mag_inv_ = 1./fabs(sp_mag_);
sp_style_ = CONSTANT;
+>>>>>>> upstream/3.0.0
}
- iarg_++;
+ ++iarg_;
hasargs = true;
} else if(strcmp(arg[iarg_],"axis") == 0) {
if (narg < iarg_+4) error->fix_error(FLERR,this,"not enough arguments for 'axis'");
@@@ -530,18 -465,9 +554,17 @@@ void FixMeshSurfaceStressServo::final_i
modify->addstep_compute(update->ntimestep + 1);
+<<<<<<< HEAD
+ set_point_ = -input->variable->compute_equal(sp_var_);
+ if (set_point_ == 0.) error->fix_error(FLERR,this,"Set point (desired force/torque/shear) has to be != 0.0");
+ set_point_inv_ = 1./fabs(set_point_);
+
+ modify->addstep_compute(update->ntimestep + 1);
+=======
}
+>>>>>>> upstream/3.0.0
- // auto mode
-
+ // auto mode - p-controller with variable proportional gain
if (mode_flag_) {
pv_mag_ = vectorDot3D(pv_vec_,axis_);
diff --cc src/general_container.h
index 34d0507,764669e..b7a0514
--- a/src/general_container.h
+++ b/src/general_container.h
@@@ -130,15 -136,13 +136,18 @@@ namespace LAMMPS_N
inline void clearContainer()
{ numElem_ = 0; }
+ inline void setDefaultValue(T val)
+ { defaultValue_ = val; useDefault_ = true; }
+
protected:
+<<<<<<< HEAD
+ GeneralContainer(char *_id);
+ GeneralContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
+=======
GeneralContainer(const char *_id);
GeneralContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
+>>>>>>> upstream/3.0.0
GeneralContainer(GeneralContainer<T,NUM_VEC,LEN_VEC> const &orig);
virtual ~GeneralContainer();
diff --cc src/general_container_I.h
index 074c7cb,dde9a9d..737bad9
--- a/src/general_container_I.h
+++ b/src/general_container_I.h
@@@ -33,14 -37,11 +37,15 @@@
------------------------------------------------------------------------- */
template<typename T, int NUM_VEC, int LEN_VEC>
+<<<<<<< HEAD
+ GeneralContainer<T,NUM_VEC,LEN_VEC>::GeneralContainer(char *_id)
+=======
GeneralContainer<T,NUM_VEC,LEN_VEC>::GeneralContainer(const char *_id)
+>>>>>>> upstream/3.0.0
: ContainerBase(_id),
numElem_(0),
- maxElem_(GROW)
+ maxElem_(GROW),
+ defaultValue_(0)
{
create<T>(arr_,GROW,NUM_VEC,LEN_VEC);
}
diff --cc src/neigh_gran.cpp
index f51f301,86c45ec..a7580bd
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@@ -462,23 -460,21 +466,23 @@@ void Neighbor::granular_bin_no_newton_g
void Neighbor::granular_bin_no_newton(NeighList *list)
{
- int i,j,k,m,n,nn,ibin,d;
+ int i,j,k,m,n,nn=0,ibin,d;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
- int *neighptr,*touchptr;
- double *shearptr;
+ int *neighptr,*touchptr = NULL;
+ double *shearptr = NULL;
NeighList *listgranhistory;
- int *npartner,**partner;
- double **contacthistory;
- int **firsttouch;
- double **firstshear;
- MyPage<int> *ipage_touch;
- MyPage<double> *dpage_shear;
- int dnum;
+ int *npartner = NULL,**partner = NULL;
+ double **contacthistory = NULL;
+ int **firsttouch = NULL;
+ double **firstshear = NULL;
+ MyPage<int> *ipage_touch = NULL;
+ MyPage<double> *dpage_shear = NULL;
+ int dnum = 0;
+ double contactHistoryDistanceFactorSqr = contactHistoryDistanceFactor*contactHistoryDistanceFactor;
+
// bin local & ghost atoms
bin_atoms();
diff --cc src/scalar_container.h
index cf95de5,2d7a0cb..5bdc2bc
--- a/src/scalar_container.h
+++ b/src/scalar_container.h
@@@ -38,13 -42,9 +42,17 @@@ namespace LAMMPS_N
class ScalarContainer : public GeneralContainer <T, 1, 1>
{
public:
+<<<<<<< HEAD
++<<<<<<< HEAD
+ ScalarContainer(char *_id);
+ ScalarContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
+=======
++=======
+ ScalarContainer();
++>>>>>>> upstream/3.1.0+repack1
ScalarContainer(const char *_id);
ScalarContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
+>>>>>>> upstream/3.0.0
ScalarContainer(ScalarContainer<T> const &orig);
virtual ~ScalarContainer();
@@@ -65,11 -67,14 +75,21 @@@
------------------------------------------------------------------------- */
template<typename T>
+<<<<<<< HEAD
++<<<<<<< HEAD
+ ScalarContainer<T>::ScalarContainer(char *_id)
+=======
++=======
+ ScalarContainer<T>::ScalarContainer()
+ : GeneralContainer<T,1,1>(0)
+ {
+
+ }
+
+ template<typename T>
++>>>>>>> upstream/3.1.0+repack1
ScalarContainer<T>::ScalarContainer(const char *_id)
+>>>>>>> upstream/3.0.0
: GeneralContainer<T,1,1>(_id)
{
--
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