Dislocation engineering release

Makefile

@@ -1,4 +1,4 @@
-CUDA_HOME = /usr/local/cuda
+CUDA_HOME = /apps/free/cuda/7.5.18/
 GPU_ARCH	= sm_30
 OS:=	$(shell uname)
 ifeq ($(OS),Darwin)

bin/run.sh

@@ -29,10 +29,10 @@
 #SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #!/bin/bash
 i=0
-EMAIL=[email protected]
+EMAIL=$1
 count=0
-NAME=$1
-PARAMS=$2
+NAME=$2
+PARAMS=$3
 declare -a JOBS=(-1 -1 -1 -1 -1 -1 -1 -1)
 function run_gpue_test {
 	echo $1
@@ -54,15 +54,14 @@ function run_gpue {
 	cd ./$NAME$A
 	pwd >> result.log
 	echo $1 >>result.log
-	mail -s "#Started GPU Job# $A" [email protected] < result.log
+	mail -s "#Started GPU Job# $A" ${EMAIL} < result.log
 	./gpue $1 2>&1> result.log
 	mkdir -p ./images
 	#python ./py/vis.py >> result.log
 	cp *.png ./images
 	cd ./images
 	ls | grep wfc_evr | grep _abs | grep png | sort -k3 -t _ -n > list1.txt;mencoder mf://@list1.txt -mf w=1280:h=1024:fps=24:type=png -oac copy -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:mv0:trell:v4mv:cbp:last_pred=3:predia=2:dia=2:vmax_b_frames=2:vb_strategy=1:precmp=2:cmp=2:subcmp=2:preme=2:qns=2:vbitrate=10000000 -o wfc_${PWD##*/}.avi
 	rm -rf ./*.png
-	#python ./py/hist3d.py
 	rm wfc*
 	mail -s "#Completed GPU Job# $A" $EMAIL < $(echo $(cat result.log; cat ./Params.dat))
 	cd ../../../../..

bin/run_params.conf

@@ -51,12 +51,17 @@
 #    vortex creation.
 # -X, -Y are omega_x and omega_y (omega_perp when both are equal)
 # -k is the potential kick mode. 0 is off, 1 is periodic, 2 is single.
-# -O is the kicking potential rotation angle.
+# -O is the kicking potential/kill vortex relative phase rotation angle.
 # -S is the kicking potential lattice spacing scaling.
 # -W turns on or off the wavefunction output printing.
 # -V, -U are the x and y shifts of the kicking potential.
+# -a, turns on the graph calculation code. Necessary for vortex annihilation
+# -K, selects vortex with specified UID for termination. Plot adjacency matrix of initial state to determine which index (graph_0 --- need to do simulation before you get this; will be updated at some point)
+# -D, sets offset for kill vortex distance radially
 
--x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 0 -e 2e5 -p 1000 -r 1 -w 0.995 -o 100 -d 4 -l 1 -s 1 -i 1.0 -P 10000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0
--x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 0 -e 2e5 -p 1000 -r 1 -w 0.995 -o 100 -d 4 -l 1 -s 1 -i 1.0 -P 15000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0
--x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 0 -e 2e5 -p 1000 -r 1 -w 0.995 -o 100 -d 4 -l 1 -s 1 -i 1.0 -P 20000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0
--x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 0 -e 2e5 -p 1000 -r 1 -w 0.995 -o 100 -d 4 -l 1 -s 1 -i 1.0 -P 25000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0
+
+# Sample simulation data sets
+-x 256 -y 256 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.65 -o 100 -d 0 -l 1 -s 1 -i 1.0 -P 10000.0 -G 1.0 -L 10 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 1 -D 0.0
+-x 512 -y 512 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.75 -o 100 -d 1 -l 1 -s 1 -i 1.0 -P 15000.0 -G 1.0 -L 20 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 2 -D 1.0
+-x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.85 -o 100 -d 2 -l 1 -s 1 -i 1.0 -P 20000.0 -G 1.0 -L 30 -X 6.28318 -Y 6.28318 -k 0 -O 20.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 3 -D -4.5
+-x 2048 -y 2048 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.95 -o 100 -d 3 -l 1 -s 1 -i 1.0 -P 25000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 0 -K 0 -D 0

py/vis.py

@@ -31,7 +31,7 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 '''
 import os
-CPUs = 4# os.environ['SLURM_JOB_CPUS_PER_NODE']
+CPUs = os.environ['SLURM_JOB_CPUS_PER_NODE']
 print "Number of cores: " + str(CPUs)
 from numpy import genfromtxt
 import math as m
@@ -320,13 +320,6 @@ def overlap(dataName, initValue, finalValue, increment):
 		print i, np.sum(b)
 
 if __name__ == '__main__':
-	try:
-		delaunay('vort_arr_',0)
-		stats.lsFit(0,evMaxVal,incr)
-		hist3d.plot_hist_pcolor(0,evMaxVal,incr,'b')
-		vort_traj('traj_plot',200)
-	except:
-		print "Unhandled error occurred. Blame Lee."
 	opPot('V_opt_0',200)
 	opPot('V_0',200)
 	opPot('K_0',200)
@@ -345,10 +338,6 @@ def overlap(dataName, initValue, finalValue, increment):
 	while evImgList:
 		i=evImgList.pop()
 		ev_proc.append(Process(target=image_gen_single,args=("wfc_ev",i,200,0b101000)))
-		#ev_proc.append(Process(target=mpld3.show,))
-		ev_proc.append(Process(target=delaunay,args=("vort_lsq_",'.csv',i)))
-		ev_proc.append(Process(target=voronoi,args=("vort_lsq_",'.csv',i)))
-		ev_proc.append(Process(target=hist_gen,args=("hist_ev",i,128)))
 	proc = gnd_proc + ev_proc
 	while proc:
 		#if (mp.cpu_count()/2) > len(mp.active_children()):

py/vort.py

@@ -188,7 +188,7 @@ def idx_min_dist(self,vortex, isSelf=False): #Closest vtx to self
 		return (ret_idx,r)
 
 ###############################################################################
-	def remove(self,pos): #Remove vortices outside articificial boundary
+	def remove(self,pos): #Remove vortices outside artificial boundary
 ###############################################################################
 		if self.length > 1 and pos > 1:
 			current = self.element(pos-1).next

src/split_op.cu

@@ -48,7 +48,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 unsigned int LatticeGraph::Edge::suid = 0;
 unsigned int LatticeGraph::Node::suid = 0;
-
+double DX = 0.0;
 char buffer[100];
 int verbose; //Print more info. Not curently implemented.
 int device; //GPU ID choice.
@@ -64,7 +64,7 @@ double x0_shift, y0_shift; //Optical lattice shift parameters.
 double Rxy; //Condensate scaling factor.
 double a0x, a0y; //Harmonic oscillator length in x and y directions
 double sepMinEpsilon=0.0; //Minimum separation for epsilon.
-
+int kill_idx = -1;;
 /*
  * Checks CUDA routines have exitted correctly.
  */
@@ -395,7 +395,7 @@ int evolve( cufftDoubleComplex *gpuWfc,
 				case 2: //Real-time evolution, constant Omega value.
 					fileName = "wfc_ev";
 			        vortexLocation = (int *) calloc(xDim * yDim, sizeof(int));
-			        num_vortices[0] = Tracker::findVortex(vortexLocation, wfc, 1e-4, xDim, x, i);
+			        num_vortices[0] = Tracker::findVortex(vortexLocation, wfc, 2e-4, xDim, x, i);
 
 			        if (i == 0) { //If initial step, locate vortices, least-squares to find exact centre, calculate lattice angle, generate optical lattice.
 				        vortCoords = (struct Vtx::Vortex *) malloc(
@@ -447,14 +447,15 @@ int evolve( cufftDoubleComplex *gpuWfc,
 				        }
 				        if(i==0) {
 					        //Lambda for vortex annihilation/creation.
-					        auto killIt=[&](int idx) {
-					            WFC::phaseWinding(Phi, 1, x, y, dx, dy, lattice.getVortexUid(idx)->getData().coordsD.x,
-					                          lattice.getVortexUid(idx)->getData().coordsD.y, xDim);
+					        auto killIt=[&](int idx, int winding, double delta_x) {
+					            WFC::phaseWinding(Phi, winding, x, y, dx, dy, lattice.getVortexUid(idx)->getData().coordsD.x + cos(angle_sweep + vort_angle)*delta_x,
+					                          lattice.getVortexUid(idx)->getData().coordsD.y + sin(angle_sweep + vort_angle)*delta_x, xDim);
 					            cudaMemcpy(Phi_gpu, Phi, sizeof(double) * xDim * yDim, cudaMemcpyHostToDevice);
 					            cMultPhi <<<grid, threads>>> (gpuWfc, Phi_gpu, gpuWfc);
-				            };
-					        //killIt(44); //Kills vortex with UID 44
-
+				        	};
+						if (kill_idx > 0){
+							killIt(kill_idx,1,DX); //Kills vortex with UID idx 
+						}
 
 				        }
 				        lattice.createEdges(1.5 * 2e-5 / dx);
@@ -768,7 +769,7 @@ template<typename T> void parSum(T *gpuToSumArr, T *gpuParSum, int xDim, int yDi
 //###################################################################################################################
 int parseArgs(int argc, char** argv){
 	int opt;
-	while ((opt = getopt (argc, argv, "d:x:y:w:G:g:e:T:t:n:p:r:o:L:l:s:i:P:X:Y:O:k:W:U:V:S:a:")) != -1) {
+	while ((opt = getopt (argc, argv, "D:d:x:y:w:G:g:e:T:t:n:p:r:o:L:l:s:i:P:X:Y:O:k:W:U:V:S:a:K:")) != -1) {
 		switch (opt)
 		{
 			case 'x':
@@ -906,6 +907,16 @@ int parseArgs(int argc, char** argv){
 				printf("Argument for graph is %d\n",graph);
 				appendData(&params,"graph",graph);
 				break;
+			case 'K':
+				kill_idx = atoi(optarg);
+				printf("Argument for kill_idx is %d\n",kill_idx);
+				appendData(&params,"kill_idx",kill_idx);
+				break;
+			case 'D':
+				DX = atoi(optarg);
+				printf("Argument for DX is %d\n",DX);
+				appendData(&params,"DX",DX);
+				break;
 			case '?':
 				if (optopt == 'c') {
 					fprintf (stderr, "Option -%c requires an argument.\n", optopt);

src/tracker.cc

@@ -298,7 +298,7 @@ namespace Tracker {
 				location = i;
 			}
 		}
-		double ang=(fmod(atan2( (vortCoords[location].coords.y - central.coords.y), (vortCoords[location].coords.x - central.coords.x) ),PI/3));
+		double ang=0;//(fmod(atan2( (vortCoords[location].coords.y - central.coords.y), (vortCoords[location].coords.x - central.coords.x) ),PI/3));
 		printf("Angle=%e\n",ang);
 		return PI/3 - ang;