source: issm/trunk-jpl/jenkins/examples_tests.sh@ 27553

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1#!/bin/bash
2################################################################################
3# This script runs the examples tests (i.e. contents of examples directory,
4# which are implementations of the tutorials found at
5# https://issm.jpl.nasa.gov/documentation/tutorials/). It is intended to be
6# called from jenkins/jenkins.sh.
7#
8# runme files are modified as needed to fill in statements that would otherwise
9# be added by user.
10#
11# NOTE:
12# - Indentation of replacement string literals (e.g. 'STEP_EIGHT') is set to
13# nest cleanly in this file, but will result in unclean nesting in the runme
14# files (which should not be an issue)
15# - Single-line string replacements in runme.m can effectively be performed
16# using sed. When performing multi-line replacements, perl is a better
17# option.
18#
19# TODO:
20# - Figure out how to remove \ and \n\ from multiline string variables while
21# preserving formatting when value is printed to file.
22################################################################################
23
24## Constants
25#
26RUNME_FILE='runme.m'
27RUN_EXAMPLE=0
28STATUS_HANDLING="\
29 disp('SUCCESS');\n\
30 catch me\n\
31 message=getReport(me);\n\
32 fprintf('%s',message);\n\
33 disp('FAILURE');\n\
34 end\n\
35 exit\n\
36"
37
38cd $ISSM_DIR/examples
39
40for dir in ./* ; do
41 if [ -d "${dir}" ]; then
42 # # Temporary short circuit to check single example
43 # example="./AMR"
44 # if [ "${dir}" != "${example}" ]; then
45 # continue
46 # fi
47
48 # Some of the examples are incomplete (on purpose). As such, we will
49 # have to populate the missing steps in order to make sure that
50 # everything is working.
51
52 cd ${dir}
53 if [ "${dir}" == "./AMR" ]; then
54 sed -i.bak -e '1 s|^.*$|try\n\n&|' $RUNME_FILE
55 RUN_EXAMPLE=1
56 elif [ "${dir}" == "./Data" ]; then
57 echo 'Directory contains datasets only; no example to run.'
58 RUN_EXAMPLE=0
59 elif [ "${dir}" == "./EsaGRACE" ]; then
60 sed -i.bak -e 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
61 RUN_EXAMPLE=1
62 elif [ "${dir}" == "./EsaWahr" ]; then
63 sed -i.bak -e 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
64 RUN_EXAMPLE=1
65 elif [ "${dir}" == "./Functions" ]; then
66 echo "Directory contains functions only; no example to run."
67 RUN_EXAMPLE=0
68 elif [ "${dir}" == "./Greenland" ]; then
69 # STEP_SEVEN #{{{
70 STEP_SEVEN="\
71 if any(steps==7)\n\
72 disp(' Step 7: Historical Relaxation run');\n\
73 md = loadmodel('./Models/Greenland.Control_drag');\n\
74 \n\
75 load smbbox\n\
76 \n\
77 %convert mesh x,y into the Box projection\n\
78 [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71);\n\
79 [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70);\n\
80 \n\
81 %Interpolate and set surface mass balance\n\
82 index = BamgTriangulate(x1(:),y1(:));\n\
83 smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi);\n\
84 smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice;\n\
85 md.smb.mass_balance = [smb;1 ];\n\
86 \n\
87 %Set transient options, run for 20 years, saving every 5 timesteps\n\
88 md.timestepping.time_step=0.2;\n\
89 md.timestepping.final_time=200;\n\
90 md.settings.output_frequency=5;\n\
91 \n\
92 %Additional options\n\
93 md.inversion.iscontrol=0;\n\
94 md.transient.requested_outputs={'IceVolume','TotalSmb', ...\n\
95 'SmbMassBalance'};\n\
96 md.verbose=verbose('solution',true,'module',true);\n\
97 \n\
98 %Go solve\n\
99 md.cluster=generic('name',oshostname,'np',2);\n\
100 md=solve(md,'Transient');\n\
101 \n\
102 save ./Models/Greenland.HistoricTransient_200yr md;\n\
103 end\n\
104 "
105 #}}}
106 # STEP_EIGHT #{{{
107 STEP_EIGHT="\
108 if any(steps==8)\n\
109 %Load historic transient model\n\
110 md=loadmodel('./Models/Greenland.HistoricTransient_200yr');\n\
111 \n\
112 %Create Line Plots of relaxation run. Create a figure.\n\
113 figure;\n\
114 \n\
115 %Save surface mass balance, by looping through 200 years (1000 steps)\n\
116 %Note, the first output will always contain output from time step 1\n\
117 surfmb=[];\n\
118 for i=2:201;\n\
119 surfmb=[surfmb md.results.TransientSolution(i).SmbMassBalance];\n\
120 end\n\
121 \n\
122 %Plot surface mass balance time series in first subplot\n\
123 subplot(3,1,1);\n\
124 plot([1:200],mean(surfmb));\n\
125 \n\
126 %Title this plot Mean surface mass balance\n\
127 title('Mean Surface mass balance');\n\
128 \n\
129 %Save velocity by looping through 200 years\n\
130 vel=[];\n\
131 for i=2:201;\n\
132 vel=[vel md.results.TransientSolution(i).Vel];\n\
133 end\n\
134 \n\
135 %Plot velocity time series in second subplot\n\
136 subplot(3,1,2);\n\
137 plot([1:200],mean(vel));\n\
138 \n\
139 %Title this plot Mean Velocity\n\
140 title('Mean Velocity');\n\
141 \n\
142 %Save Ice Volume by looping through 200 years\n\
143 volume=[];\n\
144 for i=2:201;\n\
145 volume=[volume md.results.TransientSolution(i).IceVolume];\n\
146 end\n\
147 \n\
148 %Plot volume time series in third subplot\n\
149 subplot(3,1,3);\n\
150 plot([1:200],volume);\n\
151 \n\
152 %Title this plot Mean Velocity and add an x label of years\n\
153 title('Ice Volume');\n\
154 xlabel('years');\n\
155 end\n\
156 "
157 #}}}
158 sed -i.bak -e 's|steps=\[1\];|steps=\[1:8\];\n\ntry\n|' $RUNME_FILE
159 perl -0755 -p -i -e "s|if any\(steps==7\).*% step 7 end|${STEP_SEVEN}|s" $RUNME_FILE
160 perl -0755 -p -i -e "s|if any\(steps==8\).*% step 8 end|${STEP_EIGHT}|s" $RUNME_FILE
161 RUN_EXAMPLE=1
162 elif [ "${dir}" == "./IceBridge" ]; then
163 sed -i.bak -e 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
164 perl -0755 -p -i -e "s|\n\t%Mesh greenland without.*return;\n||s" $RUNME_FILE
165 RUN_EXAMPLE=1
166 elif [ "${dir}" == "./IceflowModels" ]; then
167 sed -i.bak -e '1 s|^.*$|try\n\n&|' $RUNME_FILE
168 RUN_EXAMPLE=1
169 elif [ "${dir}" == "./Inversion" ]; then
170 sed -i.bak -e 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
171 RUN_EXAMPLE=1
172 elif [ "${dir}" == "./ISMIP" ]; then
173 # TODO:
174 # - Run test again with ISMIPF configuration (will likely need to
175 # add conditional after 'RUN_EXAMPLE -eq 1' block)
176 #
177
178 # RUNME #{{{
179 RUNME="\
180 try\n\
181 %which steps to perform; steps are from 1 to 8\n\
182 %step 7 is specific to ISMIPA\n\
183 %step 8 is specific to ISMIPF\n\
184 \n\
185 steps=[1:7]; %ISMIPA\n\
186 %steps=[1:6,8]; %ISMIPF\n\
187 \n\
188 % parameter file to be used, choose between IsmipA.par or IsmipF.par\n\
189 ParamFile='IsmipA.par';\n\
190 %ParamFile='IsmipF.par';\n\
191 \n\
192 %Run Steps\n\
193 \n\
194 %Mesh Generation #1\n\
195 if any(steps==1)\n\
196 %initialize md as a new model #help model\n\
197 %->\n\
198 md=model();\n\
199 % generate a squaremesh #help squaremesh\n\
200 % Side is 80 km long with 20 points\n\
201 %->\n\
202 if(ParamFile=='IsmipA.par'),\n\
203 md=squaremesh(md,80000,80000,20,20);\n\
204 elseif(ParamFile=='IsmipF.par'),\n\
205 md=squaremesh(md,100000,100000,30,30);\n\
206 end\n\
207 % plot the given mesh #plotdoc\n\
208 %->\n\
209 plotmodel(md,'data','mesh')\n\
210 % save the given model\n\
211 %->\n\
212 save ./Models/ISMIP.Mesh_generation md;\n\
213 end\n\
214 \n\
215 %Masks #2\n\
216 if any(steps==2)\n\
217 % load the preceding step #help loadmodel\n\
218 % path is given by the organizer with the name of the given step\n\
219 %->\n\
220 md = loadmodel('./Models/ISMIP.Mesh_generation');\n\
221 % set the mask #help setmask\n\
222 % all MISMIP nodes are grounded\n\
223 %->\n\
224 md=setmask(md,'','');\n\
225 % plot the given mask #md.mask to locate the field\n\
226 %->\n\
227 plotmodel(md,'data',md.mask.ocean_levelset);\n\
228 % save the given model\n\
229 %->\n\
230 save ./Models/ISMIP.SetMask md;\n\
231 end\n\
232 \n\
233 %Parameterization #3\n\
234 if any(steps==3)\n\
235 % load the preceding step #help loadmodel\n\
236 % path is given by the organizer with the name of the given step\n\
237 %->\n\
238 md = loadmodel('./Models/ISMIP.SetMask');\n\
239 % parametrize the model # help parameterize\n\
240 % you will need to fil-up the parameter file defined by the\n\
241 % ParamFile variable\n\
242 %->\n\
243 md=parameterize(md,ParamFile);\n\
244 % save the given model\n\
245 %->\n\
246 save ./Models/ISMIP.Parameterization md;\n\
247 end\n\
248 \n\
249 %Extrusion #4\n\
250 if any(steps==4)\n\
251 \n\
252 % load the preceding step #help loadmodel\n\
253 % path is given by the organizer with the name of the given step\n\
254 %->\n\
255 md = loadmodel('./Models/ISMIP.Parameterization');\n\
256 % vertically extrude the preceding mesh #help extrude\n\
257 % only 5 layers exponent 1\n\
258 %->\n\
259 md=extrude(md,5,1);\n\
260 % plot the 3D geometry #plotdoc\n\
261 %->\n\
262 plotmodel(md,'data',md.geometry.base)\n\
263 % save the given model\n\
264 %->\n\
265 save ./Models/ISMIP.Extrusion md;\n\
266 end\n\
267 \n\
268 %Set the flow computing method #5\n\
269 if any(steps==5)\n\
270 \n\
271 % load the preceding step #help loadmodel\n\
272 % path is given by the organizer with the name of the given step\n\
273 %->\n\
274 md = loadmodel('./Models/ISMIP.Extrusion');\n\
275 % set the approximation for the flow computation #help setflowequation\n\
276 % We will be using the Higher Order Model (HO)\n\
277 %->\n\
278 md=setflowequation(md,'HO','all');\n\
279 % save the given model\n\
280 %->\n\
281 save ./Models/ISMIP.SetFlow md;\n\
282 end\n\
283 \n\
284 %Set Boundary Conditions #6\n\
285 if any(steps==6)\n\
286 \n\
287 % load the preceding step #help loadmodel\n\
288 % path is given by the organizer with the name of the given step\n\
289 %->\n\
290 md = loadmodel('./Models/ISMIP.SetFlow');\n\
291 % dirichlet boundary condition are known as SPCs\n\
292 % ice frozen to the base, no velocity #md.stressbalance\n\
293 % SPCs are initialized at NaN one value per vertex\n\
294 %->\n\
295 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);\n\
296 %->\n\
297 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);\n\
298 %->\n\
299 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);\n\
300 % extract the nodenumbers at the base #md.mesh.vertexonbase\n\
301 %->\n\
302 basalnodes=find(md.mesh.vertexonbase);\n\
303 % set the sliding to zero on the bed\n\
304 %->\n\
305 md.stressbalance.spcvx(basalnodes)=0.0;\n\
306 %->\n\
307 md.stressbalance.spcvy(basalnodes)=0.0;\n\
308 % periodic boundaries have to be fixed on the sides\n\
309 % Find the indices of the sides of the domain, for x and then for y\n\
310 % for x\n\
311 % create maxX, list of indices where x is equal to max of x (use >> help find)\n\
312 %->\n\
313 maxX=find(md.mesh.x==max(md.mesh.x));\n\
314 % create minX, list of indices where x is equal to min of x\n\
315 %->\n\
316 minX=find(md.mesh.x==min(md.mesh.x));\n\
317 % for y\n\
318 % create maxY, list of indices where y is equal to max of y\n\
319 % but not where x is equal to max or min of x\n\
320 % (i.e, indices in maxX and minX should be excluded from maxY and minY)\n\
321 % but not where x is equal to max or min of x\n\
322 %->\n\
323 maxY=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x));\n\
324 % create minY, list of indices where y is equal to max of y\n\
325 %->\n\
326 minY=find(md.mesh.y==min(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x));\n\
327 % set the node that should be paired together, minX with maxX and minY with maxY\n\
328 % #md.stressbalance.vertex_pairing\n\
329 %->\n\
330 md.stressbalance.vertex_pairing=[minX,maxX;minY,maxY];\n\
331 if (ParamFile=='IsmipF.par')\n\
332 % if we are dealing with IsmipF the solution is in\n\
333 % masstransport\n\
334 md.masstransport.vertex_pairing=md.stressbalance.vertex_pairing;\n\
335 end\n\
336 % save the given model\n\
337 %->\n\
338 save ./Models/ISMIP.BoundaryCondition md;\n\
339 end\n\
340 \n\
341 %Solving #7\n\
342 if any(steps==7)\n\
343 % load the preceding step #help loadmodel\n\
344 % path is given by the organizer with the name of the given step\n\
345 %->\n\
346 md = loadmodel('./Models/ISMIP.BoundaryCondition');\n\
347 % Set cluster #md.cluster\n\
348 % generic parameters #help generic\n\
349 % set only the name and number of process\n\
350 %->\n\
351 md.cluster=generic('name',oshostname(),'np',2);\n\
352 % Set which control message you want to see #help verbose\n\
353 %->\n\
354 md.verbose=verbose('convergence',true);\n\
355 % Solve #help solve\n\
356 % we are solving a StressBalanc\n\
357 %->\n\
358 md=solve(md,'Stressbalance');\n\
359 % save the given model\n\
360 %->\n\
361 save ./Models/ISMIP.StressBalance md;\n\
362 % plot the surface velocities #plotdoc\n\
363 %->\n\
364 plotmodel(md,'data',md.results.StressbalanceSolution.Vel)\n\
365 end\n\
366 \n\
367 %Solving #8\n\
368 if any(steps==8)\n\
369 % load the preceding step #help loadmodel\n\
370 % path is given by the organizer with the name of the given step\n\
371 %->\n\
372 md = loadmodel('./Models/ISMIP.BoundaryCondition');\n\
373 % Set cluster #md.cluster\n\
374 % generic parameters #help generic\n\
375 % set only the name and number of process\n\
376 %->\n\
377 md.cluster=generic('name',oshostname(),'np',2);\n\
378 % Set which control message you want to see #help verbose\n\
379 %->\n\
380 md.verbose=verbose('convergence',true);\n\
381 % set the transient model to ignore the thermal model\n\
382 % #md.transient \n\
383 %->\n\
384 md.transient.isthermal=0;\n\
385 % define the timestepping scheme\n\
386 % everything here should be provided in years #md.timestepping\n\
387 % give the length of the time_step (4 years)\n\
388 %->\n\
389 md.timestepping.time_step=4;\n\
390 % give final_time (20*4 years time_steps)\n\
391 %->\n\
392 md.timestepping.final_time=4*20;\n\
393 % Solve #help solve\n\
394 % we are solving a TransientSolution\n\
395 %->\n\
396 md=solve(md,'Transient');\n\
397 % save the given model\n\
398 %->\n\
399 save ./Models/ISMIP.Transient md;\n\
400 % plot the surface velocities #plotdoc\n\
401 %->\n\
402 plotmodel(md,'data',md.results.TransientSolution(20).Vel)\n\
403 end\n\
404 "
405 #}}}
406 # PAR_A #{{{
407 PAR_A="\
408 %Parameterization for ISMIP A experiment\n\
409 \n\
410 %Set the Simulation generic name #md.miscellaneous\n\
411 %->\n\
412 \n\
413 %Geometry\n\
414 disp(' Constructing Geometry');\n\
415 \n\
416 %Define the geometry of the simulation #md.geometry\n\
417 %surface is [-x*tan(0.5*pi/180)] #md.mesh\n\
418 %->\n\
419 md.geometry.surface=-md.mesh.x*tan(0.5*pi/180.);\n\
420 %base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)]\n\
421 %L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x)\n\
422 %->\n\
423 L=max(md.mesh.x)-min(md.mesh.x);\n\
424 md.geometry.base=md.geometry.surface-1000.0+500.0*sin(md.mesh.x*2.0*pi/L).*sin(md.mesh.y*2.0*pi/L);\n\
425 %thickness is the difference between surface and base #md.geometry\n\
426 %->\n\
427 md.geometry.thickness=md.geometry.surface-md.geometry.base;\n\
428 %plot the geometry to check it out\n\
429 %->\n\
430 plotmodel(md,'data',md.geometry.thickness);\n\
431 \n\
432 disp(' Defining friction parameters');\n\
433 \n\
434 %These parameters will not be used but need to be fixed #md.friction\n\
435 %one friciton coefficient per node (md.mesh.numberofvertices,1)\n\
436 %->\n\
437 md.friction.coefficient=200.0*ones(md.mesh.numberofvertices,1);\n\
438 %one friciton exponent (p,q) per element\n\
439 %->\n\
440 md.friction.p=ones(md.mesh.numberofelements,1);\n\
441 %->\n\
442 md.friction.q=ones(md.mesh.numberofelements,1);\n\
443 \n\
444 disp(' Construct ice rheological properties');\n\
445 \n\
446 %The rheology parameters sit in the material section #md.materials\n\
447 %B has one value per vertex\n\
448 %->\n\
449 md.materials.rheology_B=6.8067e7*ones(md.mesh.numberofvertices,1);\n\
450 %n has one value per element\n\
451 %->\n\
452 md.materials.rheology_n=3*ones(md.mesh.numberofelements,1);\n\
453 \n\
454 disp(' Set boundary conditions');\n\
455 \n\
456 %Set the default boundary conditions for an ice-sheet \n\
457 % #help SetIceSheetBC\n\
458 %->\n\
459 md=SetIceSheetBC(md);\n\
460 "
461 #}}}
462 # PAR_F #{{{
463 PAR_F="\
464 %Parameterization for ISMIP F experiment\n\
465 \n\
466 %Set the Simulation generic name #md.miscellaneous\n\
467 %->\n\
468 \n\
469 %Geometry\n\
470 disp(' Constructing Geometry');\n\
471 \n\
472 %Define the geometry of the simulation #md.geometry\n\
473 %surface is [-x*tan(3.0*pi/180)] #md.mesh\n\
474 %->\n\
475 md.geometry.surface=-md.mesh.x*tan(3.0*pi/180.0);\n\
476 %base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(10000.^2))]\n\
477 %L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x)\n\
478 %->\n\
479 L=max(md.mesh.x)-min(md.mesh.x);\n\
480 %->\n\
481 md.geometry.base=md.geometry.surface-1000.0+100.0*exp(-((md.mesh.x-L/2.0).^2.0+(md.mesh.y-L/2.0).^2.0)/(10000.^2.0));\n\
482 %thickness is the difference between surface and base #md.geometry\n\
483 %->\n\
484 md.geometry.thickness=md.geometry.surface-md.geometry.base;\n\
485 %plot the geometry to check it out\n\
486 %->\n\
487 plotmodel(md,'data',md.geometry.thickness);\n\
488 \n\
489 disp(' Defining friction parameters');\n\
490 \n\
491 %These parameters will not be used but need to be fixed #md.friction\n\
492 %one friciton coefficient per node (md.mesh.numberofvertices,1)\n\
493 %conversion from year to seconds with #md.constants.yts\n\
494 %->\n\
495 md.friction.coefficient=sqrt(md.constants.yts/(1000*2.140373*10^-7))*ones(md.mesh.numberofvertices,1);\n\
496 %one friciton exponent (p,q) per element\n\
497 %->\n\
498 md.friction.p=ones(md.mesh.numberofelements,1);\n\
499 %->\n\
500 md.friction.q=zeros(md.mesh.numberofelements,1);\n\
501 \n\
502 disp(' Construct ice rheological properties');\n\
503 \n\
504 %The rheology parameters sit in the material section #md.materials\n\
505 %B has one value per vertex\n\
506 %->\n\
507 md.materials.rheology_B=(1/(2.140373*10^-7/md.constants.yts))*ones(md.mesh.numberofvertices,1);\n\
508 %n has one value per element\n\
509 %->\n\
510 md.materials.rheology_n=1*ones(md.mesh.numberofelements,1);\n\
511 \n\
512 disp(' Set boundary conditions');\n\
513 \n\
514 %Set the default boundary conditions for an ice-sheet \n\
515 % #help SetIceSheetBC\n\
516 %->\n\
517 md=SetIceSheetBC(md);\n\
518 \n\
519 disp(' Initializing velocity and pressure');\n\
520 \n\
521 %initialize the velocity and pressurefields of #md.initialization\n\
522 %->\n\
523 md.initialization.vx=zeros(md.mesh.numberofvertices,1);\n\
524 %->\n\
525 md.initialization.vy=zeros(md.mesh.numberofvertices,1);\n\
526 %->\n\
527 md.initialization.vz=zeros(md.mesh.numberofvertices,1);\n\
528 %->\n\
529 md.initialization.pressure=zeros(md.mesh.numberofvertices,1);\n\
530 "
531 #}}}
532 perl -0755 -p -i'.bak' -e "s|^.*$|${RUNME}|s" $RUNME_FILE
533 perl -0755 -p -i'.bak' -e "s|^.*$|${PAR_A}|s" IsmipA.par
534 perl -0755 -p -i'.bak' -e "s|^.*$|${PAR_F}|s" IsmipF.par
535 RUN_EXAMPLE=1
536 elif [ "${dir}" == "./Jakobshavn" ]; then
537 sed -i.bak -e 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
538 RUN_EXAMPLE=1
539 elif [ "${dir}" == "./LcurveAnalysis" ]; then
540 sed -i.bak -e 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
541 RUN_EXAMPLE=1
542 elif [ "${dir}" == "./Mesh" ]; then
543 # NOTE: Cannot test exptool region selection without GUI
544 #
545
546 # RUNME #{{{
547 RUNME="\
548 try\n\
549 steps=[1:7];\n\
550 \n\
551 if any(steps==1) % Model\n\
552 md=model;\n\
553 end\n\
554 \n\
555 if any(steps==2) % squaremesh\n\
556 md=squaremesh(md,100,200,15,25);\n\
557 plotmodel(md,'data','mesh');\n\
558 end\n\
559 \n\
560 if any(steps==3) % roundmesh\n\
561 md=roundmesh(model,100,10);\n\
562 plotmodel(md,'data','mesh');\n\
563 end\n\
564 \n\
565 if any(steps==4) % triangle\n\
566 md=triangle(model,'Square.exp',.2);\n\
567 plotmodel(md,'data','mesh');\n\
568 end\n\
569 \n\
570 if any(steps==5) % bamg\n\
571 md=bamg(model,'domain','Square.exp','hmax',.05);\n\
572 plotmodel(md,'data','mesh');\n\
573 end\n\
574 \n\
575 if any(steps==6) % Non-Uniform mesh\n\
576 hvertices=[0.2;0.2;0.005;0.2];\n\
577 md=bamg(md,'domain','Square.exp','hvertices',hvertices);\n\
578 plotmodel(md,'data','mesh');\n\
579 end\n\
580 \n\
581 if any(steps==7) % Mesh adaptation\n\
582 md=bamg(model,'domain','Square.exp','hmax',.05);\n\
583 vel=shock(md.mesh.x,md.mesh.y);\n\
584 plotmodel(md,'data',vel,'edgecolor','w');\n\
585 \n\
586 md=bamg(model,'domain','Square.exp','hmax',.005);\n\
587 vel=shock(md.mesh.x,md.mesh.y);\n\
588 md=bamg(md,'field',vel,'err',0.05,'hmin',0.005,'hmax',0.3);\n\
589 vel=shock(md.mesh.x,md.mesh.y);\n\
590 plotmodel(md,'data',vel,'edgecolor','w');\n\
591 \n\
592 md=bamg(model,'domain','Square.exp','hmax',.005);\n\
593 vel=shock(md.mesh.x,md.mesh.y);\n\
594 md=bamg(md,'field',vel,'err',0.03,'hmin',0.005,'hmax',0.3,'gradation',3);\n\
595 vel=shock(md.mesh.x,md.mesh.y);\n\
596 plotmodel(md,'data',vel,'edgecolor','w');\n\
597 \n\
598 md=bamg(model,'domain','Square.exp','hmax',.005);\n\
599 vel=shock(md.mesh.x,md.mesh.y);\n\
600 md=bamg(md,'field',vel,'err',0.03,'hmin',0.005,'hmax',0.3,'gradation',1.3,'anisomax',1);\n\
601 vel=shock(md.mesh.x,md.mesh.y);\n\
602 plotmodel(md,'data',vel,'edgecolor','w');\n\
603 end\n\
604 \n\
605 if any(steps==8) % Mesh refinement in a specific region\n\
606 plotmodel(md,'data',vel,'edgecolor','w');\n\
607 exptool('refinement.exp');\n\
608 h=NaN*ones(md.mesh.numberofvertices,1);\n\
609 in=ContourToNodes(md.mesh.x,md.mesh.y,'refinement.exp',1);\n\
610 h(find(in))=0.02;\n\
611 plotmodel(md,'data',in,'edgecolor','w');\n\
612 \n\
613 vel=shock(md.mesh.x,md.mesh.y);\n\
614 md=bamg(md,'field',vel,'err',0.03,'hmin',0.005,'hmax',0.3,'hVertices',h);\n\
615 vel=shock(md.mesh.x,md.mesh.y);\n\
616 plotmodel(md,'data',vel,'edgecolor','w');\n\
617 end\n\
618 "
619 #}}}
620 touch $RUNME_FILE
621 perl -0755 -p -i'.bak' -e "s|^.*$|${RUNME}|s" $RUNME_FILE
622 RUN_EXAMPLE=1
623 elif [ "${dir}" == "./Pig" ]; then
624 # STEP_SIX #{{{
625 STEP_SIX="\
626 if any(steps==6)\n\
627 % Load Model\n\
628 md = loadmodel('./Models/PIG_Control_drag');\n\
629 % Disable inversion\n\
630 md.inversion.iscontrol=0;\n\
631 % Extrude Mesh\n\
632 disp(' Extruding mesh');\n\
633 number_of_layers=3;\n\
634 md=extrude(md,number_of_layers,1);\n\
635 % Set Flowequation\n\
636 disp(' Using HO Ice Flow Model');\n\
637 md=setflowequation(md,'HO','all');\n\
638 % Solve\n\
639 md=solve(md,'Stressbalance');\n\
640 % Save Model\n\
641 save ./Models/PIG_ModelHO md;\n\
642 end\n\
643 "
644 #}}}
645 mv ./DomainOutline.bkp ./DomainOutline.exp > /dev/null 2>&1
646 sed -i.bak -e 's|steps=\[1\];|steps=\[1:7\];\ntry\n|' $RUNME_FILE
647 perl -0755 -p -i -e "s|if any\(steps==6\).*% step 6 end|${STEP_SIX}|s" $RUNME_FILE
648 RUN_EXAMPLE=1
649 elif [ "${dir}" == "./Pig2" ]; then
650 STEP_NINE="\n disp('Needs work!'); exit"
651 sed -i.bak -e 's|steps=\[1\];|steps=\[1:9\];\n\ntry\n|' $RUNME_FILE
652 perl -0755 -p -i -e "s|if any\(steps==9\).*% step 9 end|${STEP_NINE}|s" $RUNME_FILE
653 RUN_EXAMPLE=0
654 elif [ "${dir}" == "./PigSensitivity" ]; then
655 # STEP_FOUR # {{{
656 STEP_FOUR="\
657 if any(steps==4)\n\
658 %Load model\n\
659 md = loadmodel('./Models/PIG_Transient');\n\
660 \n\
661 %Change external forcing basal melting rate and surface mass balance)\n\
662 md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1);\n\
663 md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1);\n\
664 md.smb.mass_balance=2*md.smb.mass_balance;\n\
665 \n\
666 %Define time steps and time span of the simulation\n\
667 md.timestepping.time_step=0.1;\n\
668 md.timestepping.final_time=10;\n\
669 \n\
670 %Request additional outputs\n\
671 md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'};\n\
672 \n\
673 %Solve\n\
674 md=solve(md,'Transient');\n\
675 \n\
676 %Plot\n\
677 plotmodel(md, 'data', md.results.TransientSolution(1).Vel,...\n\
678 'title#1', 'Velocity t=0 years (m/yr)',...\n\
679 'data', md.results.TransientSolution(end).Vel,...\n\
680 'title#2', 'Velocity t=10 years (m/yr)',...\n\
681 'data', md.results.TransientSolution(1).MaskOceanLevelset,...\n\
682 'title#3', 'Floating ice t=0 years',...\n\
683 'data', md.results.TransientSolution(end).MaskOceanLevelset,...\n\
684 'title#4', 'Floating ice t=10 years',...\n\
685 'caxis#1',([0 4500]),'caxis#2',([0 4500]),...\n\
686 'caxis#3',([-1,1]),'caxis#4',([-1,1]));\n\
687 \n\
688 %Save model\n\
689 save ./Models/PIG_SMB md;\n\
690 end\n\
691 "
692 #}}}
693 sed -i.bak -e 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
694 perl -0755 -p -i -e "s|if any\(steps==4\).*% step 4 end|${STEP_FOUR}|s" $RUNME_FILE
695 RUN_EXAMPLE=1
696 elif [ "${dir}" == "./shakti" ]; then
697 sed -i.bak -e 's|steps=\[1:3\];|steps=\[1:3\];\n\ntry\n|' $RUNME_FILE
698 RUN_EXAMPLE=1
699 elif [ "${dir}" == "./SlrFarrell" ]; then
700 # TODO: Convert from md.slr
701 sed -i.bak -e 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
702 RUN_EXAMPLE=0
703 elif [ "${dir}" == "./SlrGRACE" ]; then
704 # TODO: Convert from md.slr
705 sed -i.bak -e 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
706 RUN_EXAMPLE=0
707 elif [ "${dir}" == "./SlrGRACE_NIMS" ]; then
708 # TODO: Convert from md.slr
709 sed -i.bak -e 's|steps=\[1\];|steps=\[1:8\];\n\ntry\n|' $RUNME_FILE
710 RUN_EXAMPLE=0
711 elif [ "${dir}" == "./SquareIceShelf" ]; then
712 sed -i.bak -e '1 s|^.*$|try\n\n&|' $RUNME_FILE
713 RUN_EXAMPLE=1
714 elif [ "${dir}" == "./UncertaintyQuantification" ]; then
715 sed -i.bak -e 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
716 RUN_EXAMPLE=1
717 else
718 echo "Not implemented yet!"
719 exit 1
720 fi
721
722 if [ $RUN_EXAMPLE -eq 1 ]; then
723 echo "Testing example: $(basename $dir)"
724 LOG_RUNME_FILE="matlab_log_$(basename $dir)_examples.log"
725 echo -e ${STATUS_HANDLING} >> ${RUNME_FILE}
726 $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; runme" -logfile $ISSM_DIR/nightlylog/$LOG_RUNME_FILE
727 echo "starting: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
728 cat $ISSM_DIR/nightlylog/$LOG_RUNME_FILE >> $ISSM_DIR/nightlylog/matlab_log_examples.log
729 echo "finished: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
730 mv -f ${RUNME_FILE}.bak ${RUNME_FILE}
731 fi
732
733 # Extra clean up
734 if [ "${dir}" == "./ISMIP" ]; then
735 mv -f IsmipA.par.bak IsmipA.par
736 mv -f IsmipF.par.bak IsmipF.par
737 fi
738
739 if [ "${dir}" == "./Mesh" ]; then
740 rm -f $RUNME_FILE
741 fi
742
743 if [ "${dir}" == "./Pig" ]; then
744 mv -f DomainOutline.exp DomainOutline.bkp
745 fi
746
747 cd ..
748 fi
749done
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