[liggghts] 01/05: Imported Upstream version 3.0.1+repack
Anton Gladky
gladk at moszumanska.debian.org
Wed Apr 23 21:12:22 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository liggghts.
commit 9f574d067d0a9b81808472f6e442759230306797
Merge: ff040f2 f333916
Author: Anton Gladky <gladk at debian.org>
Date: Wed Apr 23 22:05:19 2014 +0200
Imported Upstream version 3.0.1+repack
doc/Eqs/model_b1.png | Bin 28056 -> 25479 bytes
doc/Section_gran_models.html | 2 +-
doc/Section_gran_models.txt | 3 +-
doc/dump.html | 6 +-
doc/dump.txt | 6 +-
doc/fix_heat_gran_conduction.html | 4 +-
doc/fix_heat_gran_conduction.txt | 4 +-
doc/gran_rolling_friction_epsd.html | 6 +-
doc/gran_rolling_friction_epsd.txt | 2 +-
doc/gran_rolling_friction_epsd2.html | 10 +-
doc/gran_rolling_friction_epsd2.txt | 6 +-
.../Tutorials_public/chute_wear/run.config | 9 -
.../LIGGGHTS/Tutorials_public/cohesion/run.config | 14 -
.../Tutorials_public/contactModels/run.config | 9 -
.../LIGGGHTS/Tutorials_public/conveyor/run.config | 9 -
.../Tutorials_public/heatTransfer_1/run.config | 9 -
.../Tutorials_public/heatTransfer_2/run.config | 9 -
.../Tutorials_public/hysteresis/run.config | 14 -
.../Tutorials_public/insert_stream/run.config | 9 -
.../LIGGGHTS/Tutorials_public/meshGran/run.config | 9 -
.../LIGGGHTS/Tutorials_public/mesh_tet/run.config | 9 -
.../Tutorials_public/movingMeshGran/run.config | 9 -
.../LIGGGHTS/Tutorials_public/packing/run.config | 9 -
.../LIGGGHTS/Tutorials_public/sph_1/run.config | 9 -
.../LIGGGHTS/Tutorials_public/sph_2/run.config | 9 -
src/MAKE/{Makefile.fedora => Makefile.clang} | 5 +-
src/MAKE/Makefile.fedora | 4 +-
src/MAKE/Makefile.fedora_debug | 4 +-
src/MAKE/Makefile.fedora_fpic | 4 +-
src/MAKE/Makefile.g++ | 0
src/MAKE/Makefile.g++3 | 0
src/MAKE/Makefile.linux | 0
src/MAKE/Makefile.mac | 0
src/MAKE/Makefile.mac_mpi | 0
src/MAKE/Makefile.odin | 0
src/MAKE/Makefile.serial | 0
src/MAKE/Makefile.tesla | 0
src/MAKE/Makefile.ubuntuVTK | 15 +-
src/Make.sh | 32 +-
src/POEMS/fix_poems.cpp | 805 +++++++++++++--------
src/POEMS/fix_poems.h | 14 +-
src/RIGID/fix_rigid.cpp | 12 +-
src/RIGID/fix_rigid_small.cpp | 32 +-
src/abstract_mesh.h | 2 +-
src/associative_pointer_array.h | 1 +
src/associative_pointer_array_I.h | 11 +
src/atom.cpp | 4 +-
src/atom.h | 2 +-
src/atom_vec.h | 2 +
src/atom_vec_body.cpp | 16 +-
src/atom_vec_sphere.cpp | 41 ++
src/atom_vec_sphere.h | 2 +
src/cfd_regionmodel_none.cpp | 4 +-
src/change_box.cpp | 1 -
src/cohesion_model_sjkr.h | 9 +-
src/cohesion_model_sjkr2.h | 11 +-
src/compute_angle_local.cpp | 4 +-
src/compute_bond_local.cpp | 3 +-
src/compute_cluster_atom.cpp | 5 +-
src/compute_dihedral_local.cpp | 9 +-
src/compute_gyration_molecule.cpp | 2 +-
src/compute_improper_local.cpp | 4 +-
src/compute_pair_gran_local.cpp | 10 +-
src/compute_property_local.cpp | 5 +-
src/compute_reduce.cpp | 26 +
src/compute_reduce.h | 8 +
src/compute_temp_profile.cpp | 3 +-
src/contact_interface.h | 22 +-
src/contact_models.h | 11 +
src/container_base.h | 2 +-
src/custom_value_tracker.h | 1 +
src/custom_value_tracker_I.h | 9 +
src/debug_liggghts.h | 5 +
src/domain.cpp | 2 +-
src/dump.cpp | 2 +-
src/dump_atom_vtk.cpp | 20 +-
src/dump_atom_vtk.h | 35 +-
src/dump_custom.cpp | 1 +
src/dump_dcd.cpp | 2 +-
src/dump_image.cpp | 8 +-
src/dump_mesh_vtk.cpp | 7 +-
src/fix.h | 16 +
src/fix_adapt.cpp | 13 +-
src/fix_ave_euler.cpp | 4 +-
src/fix_ave_spatial.cpp | 103 +++
src/fix_ave_spatial.h | 4 +
src/fix_box_relax.cpp | 12 +-
src/fix_cfd_coupling_convection.cpp | 45 +-
src/fix_cfd_coupling_force.cpp | 43 +-
src/fix_cfd_coupling_force.h | 3 +-
src/fix_cfd_coupling_force_implicit.cpp | 11 +-
src/fix_check_timestep_gran.cpp | 10 +-
src/fix_check_timestep_sph.cpp | 5 +-
src/fix_contact_history.cpp | 51 +-
src/fix_contact_history.h | 18 +
src/fix_contact_history_mesh.cpp | 132 +++-
src/fix_contact_history_mesh.h | 11 +-
src/fix_contact_history_mesh_I.h | 28 +-
src/fix_dummy2.h | 25 +
src/fix_gravity.cpp | 4 +-
src/fix_heat_gran.cpp | 56 +-
src/fix_heat_gran.h | 1 -
src/fix_heat_gran_conduction.cpp | 47 +-
src/fix_heat_gran_conduction.h | 6 +-
src/fix_insert.cpp | 3 +-
src/fix_insert_pack.cpp | 9 +-
src/fix_insert_stream.cpp | 6 +-
src/fix_massflow_mesh.cpp | 57 +-
src/fix_massflow_mesh.h | 4 +-
src/fix_mesh.cpp | 2 +-
src/fix_mesh_surface_stress.cpp | 3 +-
src/fix_mesh_surface_stress_servo.cpp | 3 +-
src/fix_move_mesh.cpp | 2 +-
src/fix_neighlist_mesh.cpp | 41 +-
src/fix_neighlist_mesh.h | 2 +-
src/fix_nh.cpp | 17 +-
src/fix_nve_sph.cpp | 4 +-
src/fix_particledistribution_discrete.cpp | 3 -
src/fix_press_berendsen.cpp | 4 +-
src/fix_property_atom_contact.h | 1 +
src/fix_property_atom_tracer.cpp | 12 +-
src/fix_property_global.cpp | 6 +-
src/fix_property_global.h | 2 +
src/fix_rigid.cpp | 12 +-
src/fix_rigid_small.cpp | 31 +-
src/fix_scalar_transport_equation.cpp | 49 +-
src/fix_scalar_transport_equation.h | 2 +
src/fix_shake.cpp | 6 +-
src/fix_sph.cpp | 2 +-
src/fix_sph_density_corr.cpp | 2 +-
src/fix_sph_pressure.cpp | 2 +
src/fix_sph_pressure.h | 5 +
src/fix_template_multiplespheres.cpp | 3 +-
src/fix_template_sphere.cpp | 1 -
src/fix_wall_gran.cpp | 20 +-
src/fix_wall_gran.h | 2 +-
src/fix_wall_gran_base.h | 37 +-
src/force.cpp | 8 -
src/general_container.h | 2 +-
src/global_properties.cpp | 78 +-
src/global_properties.h | 27 +-
src/image.cpp | 14 +-
src/input.cpp | 9 +-
src/input_mesh_tet.cpp | 2 -
src/input_mesh_tri.cpp | 1 -
src/irregular.cpp | 5 +-
src/lammps.cpp | 20 +-
src/library_cfd_coupling.cpp | 5 +-
src/math_extra_liggghts.h | 17 +
src/memory.h | 4 +-
src/mesh_mover.cpp | 12 +-
src/min.cpp | 4 -
src/min_linesearch.cpp | 4 +-
src/modified_andrew.cpp | 4 +-
src/modify.cpp | 6 +-
src/multi_node_mesh_I.h | 10 +-
src/multi_node_mesh_parallel_I.h | 15 +-
src/my_page.h | 25 +-
src/neigh_gran.cpp | 186 +++++
src/neigh_request.cpp | 15 +-
src/neigh_request.h | 4 +-
src/neigh_respa.cpp | 12 +-
src/neigh_stencil.cpp | 6 +-
src/neighbor.cpp | 20 +-
src/neighbor.h | 1 +
src/normal_model_hertz.h | 19 +-
src/normal_model_hertz_stiffness.h | 16 +-
src/normal_model_hooke.h | 21 +-
src/normal_model_hooke_hysteresis.h | 15 +-
src/normal_model_hooke_stiffness.h | 19 +-
src/pair.cpp | 76 +-
src/pair_born_coul_wolf.cpp | 4 +-
src/pair_coul_wolf.cpp | 19 +-
src/pair_gauss.cpp | 2 +-
src/pair_gran.cpp | 35 +
src/pair_gran.h | 15 +-
src/pair_gran_base.h | 42 +-
src/pair_hybrid.cpp | 20 +-
src/pair_lj_smooth_linear.cpp | 2 +-
src/pair_sph.cpp | 37 +-
src/primitive_wall.h | 2 +-
src/probability_distribution.h | 26 +-
src/procmap.cpp | 2 +-
src/property_registry.cpp | 34 +-
src/property_registry.h | 12 +-
src/read_data.cpp | 46 +-
src/read_restart.cpp | 6 +-
src/region.cpp | 6 +-
src/region_wedge.cpp | 42 +-
src/rolling_model_cdt.h | 2 +-
src/rolling_model_epsd.h | 10 +-
src/rolling_model_epsd2.h | 8 +-
src/set.cpp | 18 +-
src/settings.h | 37 +-
src/style_contact_model.blacklist | 0
src/surface_mesh_I.h | 18 +-
src/tangential_model_history.h | 8 +-
src/tangential_model_no_history.h | 2 +-
src/tracking_mesh_I.h | 2 +-
src/tri_mesh_I.h | 1 +
src/universe.cpp | 2 +-
src/variable.cpp | 22 +-
src/vector_liggghts.h | 4 +-
src/version_liggghts.h | 4 +
src/version_liggghts.txt | 4 +
src/volume_mesh_I.h | 5 +-
src/write_data.cpp | 60 +-
src/write_data.h | 2 +
src/write_restart.cpp | 2 +-
209 files changed, 2230 insertions(+), 1442 deletions(-)
diff --cc src/compute_reduce.cpp
index 24ca045,3f90b0f..1ba236a
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@@ -30,7 -37,7 +37,11 @@@ Christoph Kloss (DCS
using namespace LAMMPS_NS;
enum{SUM,MINN,MAXX,AVE};
++<<<<<<< HEAD
+enum{X,V,F,RHO,P,COMPUTE,FIX,VARIABLE};
++=======
+ enum{X,V,F,RHO,P,COMPUTE,FIX,VARIABLE};
++>>>>>>> upstream/3.0.1+repack
enum{PERATOM,LOCAL};
#define INVOKED_VECTOR 2
@@@ -111,13 -118,14 +122,20 @@@ ComputeReduce::ComputeReduce(LAMMPS *lm
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
+ } else if (strcmp(arg[iarg],"rho") == 0) {
+ which[nvalues] = RHO;
+ argindex[nvalues++] = 0;
+ } else if (strcmp(arg[iarg],"p") == 0) {
+ which[nvalues] = P;
+ argindex[nvalues++] = 0;
+ } else if (strcmp(arg[iarg],"rho") == 0) {
+ which[nvalues] = RHO;
+ argindex[nvalues++] = 0;
+ } else if (strcmp(arg[iarg],"p") == 0) {
+ which[nvalues] = P;
+ argindex[nvalues++] = 0;
+
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
@@@ -480,13 -488,13 +498,21 @@@ double ComputeReduce::compute_one(int m
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,f[i][aidx],i);
} else one = f[flag][aidx];
++<<<<<<< HEAD
+ } else if (which[m] == RHO) {
++=======
+ } else if (which[m] == RHO) {
++>>>>>>> upstream/3.0.1+repack
double *rho = atom->rho;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,rho[i],i);
} else one = rho[flag];
++<<<<<<< HEAD
+ } else if (which[m] == P) {
++=======
+ } else if (which[m] == P) {
++>>>>>>> upstream/3.0.1+repack
double *p = atom->p;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
diff --cc src/fix_ave_spatial.cpp
index 562e22c,9f6f70c..3609222
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@@ -324,8 -343,7 +343,12 @@@ FixAveSpatial::FixAveSpatial(LAMMPS *lm
filepos = ftell(fp);
}
+<<<<<<< HEAD
++<<<<<<< HEAD
+ if (fp2 && me == 0) {
++=======
+ if (fp2 && me == 0) {
++>>>>>>> upstream/3.0.1+repack
fprintf(fp2,"# Spatial-averaged data for fix %s and group %s\n",
id,arg[1]);
fprintf(fp2,"# Mean and standard deviation for all bins including between N1=%i and N2=%i particles\n",lowerLimit,upperLimit);
@@@ -339,8 -357,6 +362,11 @@@
fflush(fp2);
++<<<<<<< HEAD
+=======
+>>>>>>> upstream/3.0.0
++=======
++>>>>>>> upstream/3.0.1+repack
delete [] title1;
delete [] title2;
delete [] title3;
@@@ -907,9 -862,84 +934,85 @@@ void FixAveSpatial::end_of_step(
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
+>>>>>>> upstream/3.0.0
}
}
+
+ // calculate mean and standard deviation
+
+ if (calcStd != 0) {
+ int n_samples = 0;
+ int n_empty = 0;
+ int n_lower = 0;
+ int n_higher = 0;
+ double *true_mean, *samples_mean, *std;
+ double diff, count_sum, count_samples, samples_average, count_max;
+
+ memory->create(true_mean,nvalues,"ave/spatial:true_mean");
+ memory->create(samples_mean,nvalues,"ave/spatial:samples_mean");
+ memory->create(std,nvalues,"ave/spatial:std");
+
+ count_sum = 0;
+ count_samples = 0;
+ samples_average = 0;
+ count_max = 0;
+
+ for (i = 0; i < nvalues; i++) {
+ true_mean[i] = 0;
+
+ for (m = 0; m < nbins; m++) {
+ true_mean[i] += values_total[m][i] * count_total[m];
+ if (i == 0) count_sum += count_total[m];
+ }
+
+ if (count_sum != 0) true_mean[i] /= count_sum;
+
+ samples_mean[i] = 0;
+ std[i] = 0;
+ }
+
+ for (m = 0; m < nbins; m++) {
+ if (count_total[m] > count_max) count_max = count_total[m];
+ if (count_total[m] == 0) n_empty += 1;
+ else if (count_total[m] < lowerLimit) n_lower += 1;
+ else if (count_total[m] > upperLimit) n_higher += 1;
+ else {
+ n_samples += 1;
+ count_samples += count_total[m];
+ for (i = 0; i < nvalues; i++) {
+ samples_mean[i] += values_total[m][i];
+ diff = values_total[m][i] - true_mean[i];
+ std[i] += diff * diff;
+ }
+ }
+ }
+
+ if (n_samples != 0) {
+ for (i = 0; i < nvalues; i++) {
+ samples_average = count_samples / n_samples; // average # particles per sample
+ samples_mean[i] /= n_samples;
+ std[i] /= n_samples; // not(n_sample-1) since true_mean is the true Average
+ std[i] = sqrt(std[i]);
+ samples_mean[i] /= norm;
+ std[i] /= norm;
+ }
+ }
+
+ // output to file
+ if (fp2 && me == 0) {
+ fprintf(fp2,BIGINT_FORMAT " %g %d %g %d %d %d %d %g",
+ ntimestep,count_sum,nbins,count_max,n_empty,n_lower,n_higher,n_samples,samples_average);
+ for (i = 0; i < nvalues; i++) {
+ fprintf(fp2," %g %g %g",true_mean[i],samples_mean[i],std[i]); //;
+ }
+ fprintf(fp2,"\n");
+ fflush(fp2);
+ }
+
+ memory->destroy(true_mean);
+ memory->destroy(samples_mean);
+ memory->destroy(std);
+ }
}
/* ----------------------------------------------------------------------
diff --cc src/fix_contact_history.h
index d64c161,4b1e3b0..4063e97
--- a/src/fix_contact_history.h
+++ b/src/fix_contact_history.h
@@@ -62,15 -63,20 +63,31 @@@ class FixContactHistory : public Fix
int size_restart(int);
int maxsize_restart();
+<<<<<<< HEAD
++<<<<<<< HEAD
+ void set_index_decide_noncontacting(int index)
+ { index_decide_noncontacting = index; };
+
+ int get_dnum()
+ { return dnum; }
+=======
++=======
+ // inline access
+ inline int n_partner(int i)
+ { return npartner_[i]; }
+
+ inline int partner(int i,int j)
+ { return partner_[i][j]; }
+
+ inline void contacthistory(int i,int j,double *h)
+ { vectorCopyN(&(contacthistory_[i][j*dnum_]),h,dnum_); }
+
+ inline double* contacthistory(int i,int j)
+ { return &(contacthistory_[i][j*dnum_]); }
+
++>>>>>>> upstream/3.0.1+repack
protected:
+>>>>>>> upstream/3.0.0
int iarg_;
diff --cc src/fix_massflow_mesh.cpp
index 8a79339,c7a1af8..b091ad0
--- a/src/fix_massflow_mesh.cpp
+++ b/src/fix_massflow_mesh.cpp
@@@ -421,15 -418,6 +422,18 @@@ void FixMassflowMesh::post_integrate(
void FixMassflowMesh::pre_exchange()
{
++<<<<<<< HEAD
+ int nlocal = atom->nlocal;
+ int iPart;
+ double *counter = fix_counter_->vector_atom;
+
+<<<<<<< HEAD
+ if (update->ntimestep != next_reneighbor) return;
+
+=======
+>>>>>>> upstream/3.0.0
++=======
++>>>>>>> upstream/3.0.1+repack
if (delete_atoms_)
{
double mass_deleted_this_ = 0.;
diff --cc src/pair_sph.cpp
index 5593f0d,ab6ddca..79187a2
--- a/src/pair_sph.cpp
+++ b/src/pair_sph.cpp
@@@ -72,18 -72,11 +72,23 @@@ PairSph::PairSph(LAMMPS *lmp) : Pair(lm
mass_type = atom->avec->mass_type; // get flag for mass per type
++<<<<<<< HEAD
+ char **fixarg;
+ fixarg=new char*[11];
+ for (int kk=0;kk<11;kk++) fixarg[kk]=new char[30];
+<<<<<<< HEAD
+
+=======
+
+>>>>>>> upstream/3.0.0
+ strcpy(fixarg[0],"fgradP");
++=======
+ const char *fixarg[11];
+ fixarg[0]="fgradP";
++>>>>>>> upstream/3.0.1+repack
fixarg[1]="all";
fixarg[2]="property/atom";
- strcpy(fixarg[3],"fgradP");
+ fixarg[3]="fgradP";
fixarg[4]="vector";
fixarg[5]="yes";
fixarg[6]="yes";
diff --cc src/set.cpp
index 0beb2f2,92aeac0..8eb98a9
--- a/src/set.cpp
+++ b/src/set.cpp
@@@ -755,17 -738,12 +755,26 @@@ void Set::set(int keyword
else
{
currentTimestep = update->ntimestep;
+<<<<<<< HEAD
++<<<<<<< HEAD
+ if (currentTimestep < until)
+ {
+=======
+ if (currentTimestep < until)
+ {
+>>>>>>> upstream/3.0.0
+ if (updFix->data_style) for (int m = 0; m < nUpdValues; m++)
+ updFix->array_atom[i][m] = updValues[m];
+ else updFix->vector_atom[i]=updValues[0];
+ }
++=======
+ if (currentTimestep < until)
+ {
+ if (updFix->data_style) for (int m = 0; m < nUpdValues; m++)
+ updFix->array_atom[i][m] = updValues[m];
+ else updFix->vector_atom[i]=updValues[0];
+ }
++>>>>>>> upstream/3.0.1+repack
}
}
diff --cc src/version_liggghts.h
index c99122e,f0f3480..d9cf12d
--- a/src/version_liggghts.h
+++ b/src/version_liggghts.h
@@@ -1,5 -1,1 +1,9 @@@
+<<<<<<< HEAD
++<<<<<<< HEAD
+#define LIGGGHTS_VERSION "LIGGGHTS-PUBLIC 2.3.8, compiled 2013-10-10-16:13:21 by ckloss"
+=======
+#define LIGGGHTS_VERSION "LIGGGHTS-PUBLIC 3.0.0, compiled 2014-01-23-20:37:17 by kloss"
+>>>>>>> upstream/3.0.0
++=======
+ #define LIGGGHTS_VERSION "LIGGGHTS-PUBLIC 3.0.1, compiled 2014-04-10-19:23:58 by kloss"
++>>>>>>> upstream/3.0.1+repack
diff --cc src/version_liggghts.txt
index 46c82a8,cb2b00e..8c6b6b6
--- a/src/version_liggghts.txt
+++ b/src/version_liggghts.txt
@@@ -1,5 -1,1 +1,9 @@@
+<<<<<<< HEAD
++<<<<<<< HEAD
+2.3.8
+=======
+3.0.0
+>>>>>>> upstream/3.0.0
++=======
+ 3.0.1
++>>>>>>> upstream/3.0.1+repack
--
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