Add xgyro (#425)

* Add basic xgyro framework

* Add full CGYRO simulation logic in, and fix xgyro paths

* Add xgyro python wrapper

* Write errors on stderr

* Print sub-simulation info into out.xgyro.info

* Fix xgyro dir creation from template, and add xgyro to top Makefile

* Add regression support for xgyro

* Add xgyro reg02 and reg03

* Add support for MPI_RANK_ORDER=2, add reg test

Makefile

@@ -6,6 +6,7 @@ all:
 	cd vgen ; make
 	cd tglf ; make
 	cd cgyro ; make
+	cd xgyro ; make
 	cd gyro ; make
 	cd tgyro ; make
 	cd profiles_gen ; make
@@ -21,6 +22,7 @@ clean:
 	cd vgen ; make clean
 	cd tglf ; make clean
 	cd cgyro ; make clean
+	cd xgyro ; make clean
 	cd gyro ; make clean
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean
@@ -42,6 +44,7 @@ distclean:
 	cd neo ; make clean
 	cd tglf ; make clean
 	cd cgyro ; make clean
+	cd xgyro ; make clean
 	cd gyro ; make clean
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean

f2py/pygacode/gacodeinput.py

@@ -36,6 +36,11 @@ def add(self,param,default,n=1):
                 self.data_dict[p]=default
                 self.data_orderlist.append(p)
 
+    def rename(self,org_param,new_param):
+        self.data_dict[new_param] = self.data_dict[org_param]
+        del self.data_dict[org_param]
+        self.data_orderlist[self.data_orderlist.index(org_param)] = new_param
+
     def dep(self,param,default):
         self.dep_dict[param]=default
         self.dep_orderlist.append(param)
@@ -56,7 +61,7 @@ def printmsg(self):
     def set_extension(self,text):
         self.extension = text
 
-    def read_input(self,inputfile):
+    def read_input(self,inputfile,write_ext=True):
         # 1. read user input file
         with open(inputfile,'r') as fin:
            for line in fin.readlines():
@@ -88,8 +93,11 @@ def read_input(self,inputfile):
                 self.error=1
                 self.error_msg=self.error_msg+"ERROR: (gacodeinput) Bogus parameter "+x+'\n'
 
-        if self.error == 0:
-            with open(inputfile+self.extension,'w') as f:
+        if write_ext and (self.error == 0):
+            self.write_parsed(inputfile+self.extension)
+
+    def write_parsed(self,outfile):
+            with open(outfile,'w') as f:
                for x in self.data_orderlist:
                    f.write(self.data_dict[x]+'  '+x+'\n')
 

shared/bin/gacode_reg_do

@@ -8,6 +8,7 @@
 #
 # EXAMPLE:
 #  gacode_reg_do 2 1 0 neo 1e-5
+#  gacode_reg_do 2 1 0 xgyro/cgyro 1e-5
 #----------------------------------------------------
 
 n=$#
@@ -23,10 +24,14 @@ fi
 n_proc=${1}
 n_omp=${2}
 reset=${3}
-code=${4}
+code_raw=${4}
 tol=${5}
 scase=${6}
 
+# if a / is present in code_raw string, use the part after / to signify another code
+code=`python3 -c "import sys; print(sys.argv[1].split('/')[0])" ${code_raw}`
+code2=`python3 -c "import sys; carr=sys.argv[1].split('/'); print(carr[1] if (len(carr)==2) else '')"  ${code_raw}`
+
 echo "REGRESSION TESTING: $code"
 
 testdir=$PWD/${code}_regression_test
@@ -44,7 +49,11 @@ then
    compdir=$GACODE_ADD_ROOT/$code/tools/input
 fi
 
-precfile=out.$code.prec
+if [ "x${code2}" == "x" ]; then
+  precfile=out.${code}.prec
+else
+  precfile=out.${code2}.prec
+fi
 
 if [ "$scase" == "" ] 
 then
@@ -59,13 +68,27 @@ cd $testdir
 for sim in $list
 do
    $code -g $sim -p $testdir > out.$sim
-   rm -f $sim/$precfile
+   if [ "x${code2}" == "x" ]; then
+     rm -f $sim/$precfile
+   else
+      # this is actually a bundled test, check subdirs
+      for dname in `(cd $sim && ls -p |grep / | sed 's#/##')`; do
+         rm -f $sim/$dname/$precfile
+      done
+   fi
    if [ $n_omp -eq 1 ] && [ $n_proc -eq 1 ] ; then 
       $code -e $sim -p $testdir > out.$sim
    else
       $code -e $sim -n $n_proc -nomp $n_omp -p $testdir > out.$sim
    fi
-   gacode_reg $sim $compdir $precfile $tol
+   if [ "x${code2}" == "x" ]; then
+      gacode_reg $sim $compdir $precfile $tol
+   else
+      # this is actually a bundled test, check subdirs
+      for dname in `(cd $sim && ls -p |grep / | sed 's#/##')`; do
+         gacode_reg $sim/$dname $compdir $precfile $tol
+      done
+   fi
    if [ $reset -eq 1 ]
    then
       # Overwrite regression data with current data

shared/bin/gacode_reg_do_restart

@@ -9,6 +9,7 @@
 #
 # EXAMPLE:
 #  gacode_reg_do_restart 2 1 0 cgyro 1e-6 reg01
+#  gacode_reg_do_restart 2 1 0 xgyro/cgyro 1e-6 reg01
 #----------------------------------------------------
 
 n=$#
@@ -24,10 +25,14 @@ fi
 n_proc=${1}
 n_omp=${2}
 reset=${3}
-code=${4}
+code_raw=${4}
 tol=${5}
 scase=${6}
 
+# if a / is present in code_raw string, use the part after / to signify another code
+code=`python3 -c "import sys; print(sys.argv[1].split('/')[0])" ${code_raw}`
+code2=`python3 -c "import sys; carr=sys.argv[1].split('/'); print(carr[1] if (len(carr)==2) else '')"  ${code_raw}`
+
 echo "REGRESSION TESTING: $code"
 
 testdir=$PWD/${code}_regression_test
@@ -45,8 +50,13 @@ then
    compdir=$GACODE_ADD_ROOT/$code/tools/input
 fi
 
-precfile=out.$code.prec
-infile=input.$code
+if [ "x${code2}" == "x" ]; then
+  precfile=out.${code}.prec
+  infile=input.${code}
+else
+  precfile=out.${code2}.prec
+  infile=input.${code2}
+fi
 
 if [ "$scase" == "" ] 
 then
@@ -61,33 +71,44 @@ cd $testdir
 for sim in $list
 do
    $code -g $sim -p $testdir > out.$sim
-   rm -f $sim/$precfile
-   # patch input file to have frequent checkpointing
-   mv $sim/$infile $sim/$infile.org
-   grep -v RESTART_STEP $sim/$infile.org > $sim/$infile
-   echo "RESTART_STEP=1" >> $sim/$infile
+   if [ "x${code2}" == "x" ]; then
+     dnames="$sim"
+   else
+     dnames=`(ls -p -d ${sim}/* |grep '/$' |sed 's/.$//' )`
+   fi
+   for dname in $dnames; do
+     rm -f ${dname}/$precfile
+     # patch input file to have frequent checkpointing
+     mv ${dname}/$infile ${dname}/$infile.org
+     grep -v RESTART_STEP ${dname}/$infile.org > ${dname}/$infile
+     echo "RESTART_STEP=1" >> ${dname}/$infile
+   done
    # now run it 3 times
    for ((i=0; $i<3; i=$i+1))
    do
     if [ $i -ne 0 ]
     then
-      cp $sim/$precfile $sim/$precfile.$oi
+     for dname in $dnames; do
+      cp ${dname}/$precfile ${dname}/$precfile.$oi
+     done
     fi
     if [ $n_omp -eq 1 ] && [ $n_proc -eq 1 ] ; then 
       $code -e $sim -p $testdir > out.$sim
     else
       $code -e $sim -n $n_proc -nomp $n_omp -p $testdir > out.$sim
     fi
-    cp $sim/$precfile $sim/$precfile.$i
-    if [ $i -eq 0 ]
-    then
+    for dname in $dnames; do
+     cp ${dname}/$precfile ${dname}/$precfile.$i
+     if [ $i -eq 0 ]
+     then
       # reuse the non-checkpointed result from original regression test
       myprecfile=$precfile
-    else
+     else
       # use the additional iterations else
       myprecfile=$precfile.$i
-    fi
-    gacode_reg $sim $compdir $myprecfile $tol
+     fi
+     gacode_reg $dname $compdir $myprecfile $tol
+    done
     oi=$i
    done
    if [ $reset -eq 1 ]

shared/bin/gacode_setup

@@ -6,6 +6,7 @@
 export PATH=$GACODE_ROOT/tgyro/bin:${PATH}
 export PATH=$GACODE_ROOT/gyro/bin:${PATH}
 export PATH=$GACODE_ROOT/cgyro/bin:${PATH}
+export PATH=$GACODE_ROOT/xgyro/bin:${PATH}
 export PATH=$GACODE_ROOT/neo/bin:${PATH}
 export PATH=$GACODE_ROOT/vgen/bin:${PATH}
 export PATH=$GACODE_ROOT/tglf/bin:${PATH}

xgyro/Makefile

@@ -0,0 +1,27 @@
+#----------------------------
+# Toplevel makefile for xgyro
+#----------------------------
+
+include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
+
+export EXTRA_LIBS = \
+	${GACODE_ROOT}/cgyro/src/cgyro_lib.a \
+	${GACODE_ROOT}/f2py/expro/expro_lib.a \
+        ${GACODE_ROOT}/f2py/geo/geo_lib.a \
+        ${GACODE_ROOT}/shared/math/math_lib.a
+
+all:
+	gacode_getversion > .VERSION
+	cd ${GACODE_ROOT}/cgyro && make
+	cd src && make
+
+clean:
+	cd ${GACODE_ROOT}/modules && rm -f xgyro*.mod
+	cd src && make clean
+
+deepclean:
+	cd ${GACODE_ROOT}/cgyro && make deepclean
+	cd ${GACODE_ROOT}/modules && rm -f xgyro*.mod
+	cd src && make clean
+
+.IGNORE: