View source for RSQSim Restart and Processing Instructions

'''
== Instructions for restarting an RSQSim simulation in order to extend a catalog from where it ended ==
'''

Note: You'll need some of the R scripts from RSQSimPostProcess

1.  Create a new directory for the simulation you are setting up, and copy over the cat1.in, cat1.pbs, UCERF3.flt, UCERF3.KZero, and UCERF3.neighbors files.

2. Rename cat1.in and cat1.pbs to match the new catalog name.

3. Update the catalog name and input file name in the new cat2.pbs, and the outNameInfix in the new cat2.in files.

4. Read in catalog 1:
<pre>
eqs = readEqs("home/user/name/catalog/eqs.catalog1.out")
</pre>
5. Create the new input files for shear stress, normal stress, and theta from the end of catalog 1 and fill those in for the variables initTauFname, initSigmaFname, and initThetaFname in your cat2.in file:
<pre>
tmp = mkInitTauSigmaThetaSlipSpeed(eqs, Inf, writeTau = "final", writeSlipSpeed = 0,   
		                   initTauFile="cat2.initTau",
		                   initSigmaFile="cat2.initSigma",
	                           initThetaFile = "cat2.initTheta")
</pre>
* If the final snapshots (.out.final files) weren’t written out for cat1, but snapshots were written out during the simulations, you can change writeTau = “final” to writeTau = 2 in order to use those snapshots (out.2 files). If no snapshots were written then you’re out of luck and can’t restart that simulation.

6. Get the start time for cat2 and copy the whole number (all 22 digits) into the variable tStart in the new cat2.in file:
<pre>
tStart = format(tmp$t, digits=22) 	 
</pre>					
7.  Read or create a list of pinned patches using the variable pin:

If there is a pin file for cat1:
<pre>
pin = scan("../cat1.pin") 
</pre>
Otherwise, the pinned file is just a list of 0's (not pinned) or 1's (pinned) for each patch in the fault model, so if there isn't one, you can just create one of 0's:
<pre>
pin = rep(0, eqs$fault$np)
</pre>
8. Update pin from the list of patches that got locked in cat1 and write out the new pin file for cat2:
<pre>				
system("grep Eliminating ../*e | awk '{print $4}' > ../cat1.locked")
pin2 = scan(file="../cat1.locked")			
pin[pin2] = 1						
write(pin, file="cat2.pin", ncol=1)				
</pre>
9. Update the pinnedFname in your cat2.in file to cat2.pin

10. Update maxT in your cat2.in file to the length you want the extended catalog to be (in seconds).

=='''Instructions for combining extended/restarted catalogs into one long catalog''' ==

Note: You'll need some of the R scripts from RSQSimPostProcess 

1. Set up a list to tell R to only load the files you need (eList, pList, dList, and tList):
<pre>
L = c("e", "p", "d", "t")
</pre>		
2. Set up the list of catalogs to combine (in the order that they ran):
<pre>
eqFiles = c("home/user/name/catalog/cat1/eqs.cat1.out",
	    "home/user/name/catalog/cat2/eqs.cat2.out")
</pre>
3. Read and combine them into one catalog:
<pre>
eqs = readAndCombineEqfiles(eqFiles, returnLists=L)
</pre>
4. Write out the new eqs.out, and List files:
<pre>
writeEqsAndLists(eqs, outFnameInfix = paste("combinedCat", sep = ""))
</pre>
Note: Reading in an eqs.RData file is faster so it’s helpful save that version too. The whole combined ‘eqs’ data structure will be stored in the combinedCat.RData file:
<pre>
save(eqs, file = "combinedCat.RData")
</pre>
Final Note: Use the R function load() to read the combinedCat.RData file back in (only use readEqs.R on the eqs.out files). 
<pre>
load("combinedCat.RData")
</pre>

5. If you also saved and need to combine your transitions file:
<pre>
transFiles = c(“home/user/name/catalog/cat1/trans.cat1.out",
	       "home/user/name/catalog/cat2/trans.cat2.out")

combineTransFiles(transfiles=transFiles, outtransfile = "trans.combinedCat.out")
</pre>


== '''Instructions for filtering a catalog by magnitude and saving a new filtered catalog''' ==


1. Pick a minimum magnitude M for your new catalog (you'll get M=muse & greater):
<pre>
muse = 7 
</pre>
2. Read the full catalog in:
<pre>						 
eqs = readEqs("eqs.cat.out")			
</pre>
3. Get a list of the events >= muse
<pre>
euse = which(eqs$M>muse)
</pre>
4. Subset/filter the catalog by euse:
<pre>
eqsNew = subsetEqs(eqs,euse, renumberEvents=FALSE)
</pre>
5. Save the new filtered catalog:
<pre>
subName = "new_catalog_M7"				
writeEqsAndLists(eqsNew, outFnameInfix = paste(subName, sep = ""))
</pre>