GopherProxy

	tadd particle indexes to forcechain output - sphere - GPU-based 3D discrete ele…
	git clone git://src.adamsgaard.dk/sphere
	Log
	Files
	Refs
	LICENSE
	---
	commit 4032f0705e116464014078e8e0eb5779e4de7042
	parent 66d59542ce89a0a6c7ed15ab7a1918e017a16a90
	Author: Anders Damsgaard <[email protected]>
	Date: Thu, 21 May 2015 16:25:53 +0200

	add particle indexes to forcechain output

	Diffstat:
	M python/halfshear-darcy-creep-dynam… \| 40 +++++++++++++++++++++++++++…
	M python/sphere.py \| 2 +-
	M src/sphere.cpp \| 49 +++++++++++++++--------------…

	3 files changed, 63 insertions(+), 28 deletions(-)
	---
	diff --git a/python/halfshear-darcy-creep-dynamics.py b/python/halfshear-darcy-…
	t@@ -30,10 +30,12 @@ matplotlib.rc('grid', linestyle=':', linewidth=0.2)
	outformat='pdf'

	scatter=False
	-plotContacts=True
	+plotContacts=False
	#plotContacts=False
	plotForceChains=True
	#plotForceChains=False
	+plotHistograms=False
	+plotCombinedHistogram=True

	#sids = ['halfshear-darcy-sigma0=10000.0-k_c=2e-16-mu=2.08e-07-ss=2000.0-A=400…
	sids = ['halfshear-darcy-sigma0=10000.0-k_c=2e-16-mu=2.08e-07-ss=2000.0-A=4375…
	t@@ -232,7 +234,7 @@ for sid in sids:
	axsc1.set_rticks([])
	#axsc1.grid(False)

	- else:
	+ if plotHistograms:
	axhistload1 = fig.add_axes([Lx[sc], Ly[sc], dx, dy*.5])
	axhistload1.hist(datalists[sc][:,6], alpha=0.75, facecolor='gray',…
	#plt.yscale('log', nonposy='clip')
	t@@ -307,3 +309,37 @@ for sid in sids:
	plt.close()
	shutil.copyfile(filename, '/home/adc/articles/own/3/graphics/' + filename)
	print(filename)
	+
	+if plotCombinedHistogram:
	+ fig = plt.figure(figsize=[3.5, 3.5])
	+
	+ ax1 = plt.subplot(1, 1, 1)
	+
	+ f_min = 0.0
	+ f_max = 0.0
	+ for sc in range(len(Lx)):
	+ if f_max < numpy.max(datalists[sc][:,6]):
	+ f_max = numpy.max(datalists[sc][:,6])
	+ f_max = numpy.ceil(f_max/10.)*10.
	+ print(f_max)
	+
	+ for sc in range(len(Lx)):
	+ #axhistload1.hist(datalists[sc][:,6], alpha=0.75, facecolor='gray', lo…
	+ hist, bin_edges = numpy.histogram(datalists[sc][:,6],
	+ #numpy.arange(8),
	+ range=(f_min, f_max))
	+
	+ ax1.semilogy((bin_edges[1:] - bin_edges[:-1])/2 + bin_edges[:-1],
	+ hist, 'o-',
	+ label='$N$ = {:3.1f} kPa'.format(Ns[sc]/1000.))
	+
	+ #plt.yscale('log', nonposy='clip')
	+ ax1.set_xlabel('Contact load [N]')
	+ ax1.set_ylabel('Number of contacts')
	+ ax1.legend(loc='upper right', fancybox=True, framealpha=1.0)
	+
	+ filename = sid + '-creep-dynamics-hist.' + outformat
	+ plt.savefig(filename)
	+ plt.close()
	+ shutil.copyfile(filename, '/home/adc/articles/own/3/graphics/' + filename)
	+ print(filename)
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -5393,7 +5393,7 @@ class sim:
	plt.axvline(90. - theta_sigma1, color='k', linestyle='dashed',
	linewidth=1)
	plt.xlim([0, 90.])
	- plt.ylim([0, self.np[0]/100])
	+ plt.ylim([0, self.np[0]/10])
	#plt.xlabel('$\\boldsymbol{f}_\text{n}$ [N]')
	plt.xlabel('Contact angle [deg]')
	plt.ylabel('Count $N$')
	diff --git a/src/sphere.cpp b/src/sphere.cpp
	t@@ -13,7 +13,7 @@

	// Constructor: Reads an input binary, and optionally checks
	// and reports the values
	-DEM::DEM(const std::string inputbin,
	+DEM::DEM(const std::string inputbin,
	const int verbosity,
	const int checkVals,
	const int dry,
	t@@ -26,7 +26,7 @@ DEM::DEM(const std::string inputbin,
	using std::cout;
	using std::cerr;

	- // Extract sid from input binary filename
	+ // Extract sid from input binary filename
	size_t dotpos = inputbin.rfind('.');
	size_t slashpos = inputbin.rfind('/');
	if (slashpos - dotpos < 1) {
	t@@ -359,21 +359,21 @@ void DEM::reportValues()
	if (verbose == 1)
	cout << "double";
	} else {
	- cerr << "Error! Chosen precision not available. Check datatypes.h"
	+ cerr << "Error! Chosen precision not available. Check datatypes.h"
	<< endl;
	exit(1);
	}
	cout << " precision\n";

	- cout << " - Timestep length: time.dt = "
	+ cout << " - Timestep length: time.dt = "
	<< time.dt << " s\n"
	- << " - Start at time: time.current = "
	+ << " - Start at time: time.current = "
	<< time.current << " s\n"
	- << " - Total sim. time: time.total = "
	+ << " - Total sim. time: time.total = "
	<< time.total << " s\n"
	- << " - File output interval: time.file_dt = "
	+ << " - File output interval: time.file_dt = "
	<< time.file_dt << " s\n"
	- << " - Start at step count: time.step_count = "
	+ << " - Start at step count: time.step_count = "
	<< time.step_count << endl;

	if (params.contactmodel == 1)
	t@@ -420,8 +420,8 @@ void DEM::reportValues()
	cout << grid.num[0];
	else if (nd == 2)
	cout << grid.num[0] << " * " << grid.num[1];
	- else
	- cout << grid.num[0] << " * "
	+ else
	+ cout << grid.num[0] << " * "
	<< grid.num[1] << " * "
	<< grid.num[2];
	cout << " cells\n";
	t@@ -473,9 +473,9 @@ Float DEM::r_max()
	// Calculate the porosity with depth, and write to file in output directory
	void DEM::porosity(const int z_slices)
	{
	- // The porosity value is higher at the boundaries due
	+ // The porosity value is higher at the boundaries due
	// to the no-flux BCs.
	-
	+
	Float top;
	if (walls.nw > 0)
	top = walls.nx->w;
	t@@ -521,7 +521,7 @@ void DEM::porosity(const int z_slices)
	// Read particle values
	Float z_sphere_centre = k.x[i].z;
	Float radius = k.x[i].w;
	-
	+
	// Save vertical positions of particle boundaries
	Float z_sphere_low = z_sphere_centre - radius;
	Float z_sphere_high = z_sphere_centre + radius;
	t@@ -548,7 +548,7 @@ void DEM::porosity(const int z_slices)
	// and the centre is above the boundary
	else if (z_slice_low < z_sphere_centre && z_slice_low > z_sphe…

	- // Subtract the volume of the sphere,
	+ // Subtract the volume of the sphere,
	// then add the volume of the spherical cap below
	V_void -= V_sphere + sphericalCap(z_slice_low - z_sphere_l…
	}
	t@@ -564,15 +564,12 @@ void DEM::porosity(const int z_slices)
	// and the centre is below the boundary
	else if (z_slice_high > z_sphere_centre && z_slice_high < z_sp…

	- // Subtract the volume of the sphere,
	+ // Subtract the volume of the sphere,
	// then add the volume of the spherical cap above
	V_void -= V_sphere + sphericalCap(z_sphere_high - z_slice_…
	}
	-
	-

	}
	-
	}

	// Save the mid z-point
	t@@ -589,7 +586,7 @@ void DEM::porosity(const int z_slices)
	// Report values to stdout
	//std::cout << "z-pos" << '\t' << "porosity" << '\n';
	for (int i = 0; i<z_slices; ++i) {
	- std::cout << z_pos[i] << '\t' << porosity[i] << '\n';
	+ std::cout << z_pos[i] << '\t' << porosity[i] << '\n';
	}

	}
	t@@ -661,7 +658,7 @@ Float3 DEM::maxPos()
	}


	-// Finds all overlaps between particles,
	+// Finds all overlaps between particles,
	// returns the indexes as a 2-row vector and saves
	// the overlap size
	void DEM::findOverlaps(
	t@@ -715,7 +712,7 @@ void DEM::findOverlaps(
	}

	// Calculate force chains and generate visualization script
	-void DEM::forcechains(const std::string format, const int threedim,
	+void DEM::forcechains(const std::string format, const int threedim,
	const double lower_cutoff,
	const double upper_cutoff)
	{
	t@@ -750,7 +747,8 @@ void DEM::forcechains(const std::string format, const int …
	if (threedim == 1)
	cout << "y_2, [m]\t";
	cout << "z_2, [m]\t";
	- cout << "\|\|f_n\|\|, [N]" << endl;
	+ cout << "\|\|f_n\|\|, [N]"
	+ << "i\tj" << endl;


	} else {
	t@@ -760,7 +758,7 @@ void DEM::forcechains(const std::string format, const int …
	std::replace(s.begin(), s.end(), '.', '-');

	// Write Gnuplot header
	- cout << "#!/usr/bin/env gnuplot\n"
	+ cout << "#!/usr/bin/env gnuplot\n"
	<< "# This Gnuplot script is automatically generated using\n"
	<< "# the forcechain utility in sphere. For more information,\n"
	<< "# see https://github.com/anders-dc/sphere\n"
	t@@ -843,7 +841,8 @@ void DEM::forcechains(const std::string format, const int …
	if (threedim == 1)
	cout << k.x[j].y << '\t';
	cout << k.x[j].z << '\t';
	- cout << f_n << endl;
	+ cout << f_n
	+ << i << '\t' << j << endl;
	} else {

	// Gnuplot output
	t@@ -864,7 +863,7 @@ void DEM::forcechains(const std::string format, const int …
	cout << k.x[j].z;
	cout << " nohead "
	<< "lw " << ratio * thickness_scaling
	- << " lc palette cb " << f_n
	+ << " lc palette cb " << f_n
	<< endl;
	}
	}