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	tadd simulation constructor, fix neighbor construction - slidergrid - grid of e…
	git clone git://src.adamsgaard.dk/slidergrid
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	---
	commit 3f412993d74c736d82c909dbc66e0848fad84dc2
	parent 6fba7f184af58122623eadbe40e902759fef2a25
	Author: Anders Damsgaard <[email protected]>
	Date: Wed, 16 Mar 2016 14:25:21 -0700

	add simulation constructor, fix neighbor construction

	Diffstat:
	M debug.h \| 2 +-
	M grid.c \| 24 ++----------------------
	M grid.h \| 4 ----
	M simulation.c \| 41 +++++++++++++++++++++++++++++…
	M simulation.h \| 14 +++++++++++++-
	M test.c \| 6 +++---

	6 files changed, 60 insertions(+), 31 deletions(-)
	---
	diff --git a/debug.h b/debug.h
	t@@ -3,6 +3,6 @@

	// if defined, verbose information to stdout will be shown during the
	// slider-bond initialization function
	-#define DEBUG_FIND_AND_BOND_TO_NEIGHBORS
	+//#define DEBUG_FIND_AND_BOND_TO_NEIGHBORS

	#endif
	diff --git a/grid.c b/grid.c
	t@@ -40,11 +40,11 @@ void find_and_bond_to_neighbors_n2(
	const int N,
	const Float cutoff)
	{
	- int i, j;
	- int n_neighbors = 0;
	+ int i, j, n_neighbors;
	Float3 dist;
	Float dist_norm;
	for (i=0; i<N; i++) {
	+ n_neighbors = 0;
	for (j=0; j<N; j++) {
	if (i != j) {
	dist = subtract_float3(sliders[i].pos, sliders[j].pos);
	t@@ -69,23 +69,3 @@ void find_and_bond_to_neighbors_n2(
	}
	}
	}
	-
	-int save_slider_positions_to_file(
	- const slider* sliders,
	- const int N,
	- const char* filename)
	-{
	- FILE* f = fopen(filename, "w");
	- if (f == NULL) {
	- fprintf(stderr, "Could not open output file %s.", filename);
	- return 1;
	- }
	-
	- int i;
	- for (i=0; i<N; i++)
	- printf("%f\t%f\t%f\n",
	- sliders[i].pos.x, sliders[i].pos.y, sliders[i].pos.z);
	-
	- fclose(f);
	- return 0;
	-}
	diff --git a/grid.h b/grid.h
	t@@ -15,8 +15,4 @@ void find_and_bond_to_neighbors_n2(
	const int N,
	const Float cutoff);

	-int save_slider_positions_to_file(
	- const slider* sliders,
	- const int N,
	- const char* filename);
	#endif
	diff --git a/simulation.c b/simulation.c
	t@@ -52,10 +52,31 @@ int check_simulation_values(const simulation sim)
	return_status = 1;
	}

	+ if (sim.file_interval < 0.0) {
	+ fprintf(stderr, "Error: The output file interval"
	+ "(file_interval = %f) must be a zero or positive value.\n",
	+ sim.file_interval);
	+ return_status = 1;
	+ }
	+

	return return_status;
	}

	+simulation create_simulation()
	+{
	+ simulation sim;
	+ sim.N = 0;
	+ sim.time = 0.0;
	+ sim.time_end = 0.0;
	+ sim.dt = 0.1;
	+ sim.iteration = 0;
	+ sim.bond_length_limit = 0;
	+ sim.id = "unnamed";
	+ sim.file_interval = 0.0;
	+ return sim;
	+}
	+
	Float find_time_step(const slider* sliders, const int N, const Float safety)
	{
	Float smallest_mass = 1.0e20;
	t@@ -71,3 +92,23 @@ Float find_time_step(const slider* sliders, const int N, co…

	return safety/sqrt(largest_stiffness/smallest_mass);
	}
	+
	+int save_slider_positions_to_file(
	+ const slider* sliders,
	+ const int N,
	+ const char* filename)
	+{
	+ FILE* f = fopen(filename, "w");
	+ if (f == NULL) {
	+ fprintf(stderr, "Could not open output file %s.", filename);
	+ return 1;
	+ }
	+
	+ int i;
	+ for (i=0; i<N; i++)
	+ printf("%f\t%f\t%f\n",
	+ sliders[i].pos.x, sliders[i].pos.y, sliders[i].pos.z);
	+
	+ fclose(f);
	+ return 0;
	+}
	diff --git a/simulation.h b/simulation.h
	t@@ -11,13 +11,25 @@ typedef struct {
	Float dt;
	long int iteration;
	Float bond_length_limit;
	-
	+ char* id;
	+ Float file_interval;
	} simulation;

	+// create simulation with default values
	+simulation create_simulation();
	+
	+// calculate the longest stable time step
	Float find_time_step(const slider* sliders, const int N, const Float safety);

	+// check if simulation parameters have reasonable values
	int check_simulation_values(const simulation sim);

	+// save slider positions to a file on the disk
	+int save_slider_positions_to_file(
	+ const slider* sliders,
	+ const int N,
	+ const char* filename);
	+
	// user-defined function which sets up the simulation
	simulation setup_simulation();

	diff --git a/test.c b/test.c
	t@@ -5,13 +5,13 @@
	// test a regular, 2d, orthogonal grid of sliders
	simulation setup_simulation()
	{
	- // create empty simulation structure
	- simulation sim;
	+ // create empty simulation structure with default values
	+ simulation sim = new_simulation();

	// initialize grid of sliders
	int nx = 4;
	int ny = 4;
	- int nz = 4;
	+ int nz = 1;
	sim.N = nxnynz;
	sim.sliders = create_regular_slider_grid(nx, ny, nz, 1.0, 1.0, 1.0);