Merge pull request #17 from smsaleeb/main

Steve's updates past v6.3.03 for new tagged version v.6.3.04

Author: smsaleeb

bin.rams/RAMSIN.testonly bin.rams/RAMSIN.testrunonlybin.rams/RAMSIN.testonly renamed to bin.rams/RAMSIN.testrunonly

@@ -184,7 +184,7 @@
 
 ! History start (if RUNTYPE='HISTORY')
 
-   HFILIN   = './test.supercell/a-A-1991-04-26-213000-head.txt',
+   HFILIN   = './testrun.output/a-A-1991-04-26-213000-head.txt',
                              ! Input state file name
 
 ! Analysis file input for assimilation: 1=yes, 0=no
@@ -198,7 +198,7 @@
 !  Analysis file output
 
    IOUTPUT  =  1,             ! 0-no files, 1-write files
-   AFILEPREF  = './test.supercell/a',  
+   AFILEPREF  = './testrun.output/a',  
                               ! File prefix for all analysis files
                               !   state,mean,lite,both
 
@@ -229,10 +229,10 @@
 
 ! Input topography variables
 
-   TOPFILES = './test.supercell/toph', ! Path and prefix for topo files. 
-   SFCFILES = './test.supercell/sfch', ! Path and prefix for surface files. 
-   SSTFPFX  = './test.supercell/ssth', ! Path and prefix for sst files
-   NDVIFPFX = './test.supercell/ndh',  ! Path and prefix for ndni files
+   TOPFILES = './testrun.output/toph', ! Path and prefix for topo files. 
+   SFCFILES = './testrun.output/sfch', ! Path and prefix for surface files. 
+   SSTFPFX  = './testrun.output/ssth', ! Path and prefix for sst files
+   NDVIFPFX = './testrun.output/ndh',  ! Path and prefix for ndni files
 
    ITOPTFLG = 2,0,0,0,           ! 2 - Fill data in "leaf3_init"
    ISSTFLG  = 2,2,0,0,           ! 0 - Interpolate from coarser grid
@@ -245,8 +245,8 @@
                               ! 1 - Update values during run
 
                              ! The following only apply for IxxxxFLG=1
-   ITOPTFN  = '../../sfctypehdf5/DEM30s-h5/EL',
-              '../../sfctypehdf5/DEM30s-h5/EL',
+   ITOPTFN  = '../../sfctypehdf5/gmted2010-h5/TM',
+              '../../sfctypehdf5/gmted2010-h5/TM',
    ISSTFN   = '../../sfctypehdf5/sst-h5/S',
               '../../sfctypehdf5/sst-h5/S',
    IVEGTFN  = '../../sfctypehdf5/ogedata-h5/GE',
@@ -288,6 +288,9 @@
    IBND     = 1,             ! Lateral boundary condition flags
    JBND     = 1,             ! 1-Klemp/Wilhelmson, 2-cyclic
 
+   ISPONGE_PTS = 0,5,5,       ! Number of nested grid boundary sponge points
+   SPONGE_TAU  = 0.,30.,30.,  ! Nested grid sponge zone time scale (seconds)
+
    CPHAS    = 30.,           ! Phase speed if IBND or JBND = 1
    LSFLG    = 1,             ! Large-scale gradient flag for variables other than
                              !  normal velocity:
@@ -316,7 +319,7 @@
 
 ! KPP mixed-layer single-column ocean model
 
-   IKPP       = 1,          ! Ocean model (0-off, 1-on, 2-more diagnostics)
+   IKPP       = 0,          ! Ocean model (0-off, 1-on, 2-more diagnostics)
    DMAXKPP    = 500.,       ! Maximum ocean depth (meters)
    NKPPZ      = 48,         ! Number of ocean layers (levels = layers+1)
    DSCALEKPP  = 3.,         ! Set exponential for stretched grid
@@ -369,7 +372,7 @@
    !  9  Tall grass                  ! 20  Wetland evergreen broadleaf tree
    ! 10  Semi-desert                 ! 21  Very urban
 
-   PCTLCON  = 0.7,            ! Constant land % if for all domain
+   PCTLCON  = 1.0,            ! Constant land % if for all domain
    NSLCON   = 6,              ! Constant soil type if for all domain
 
    !   1 -- sand             2 -- loamy sand      3 -- sandy loam
@@ -536,7 +539,7 @@
 
 ! Aerosol parameters         ! See mic_init.f90 for setting profiles
                              ! ------------------------------------------
-   IAEROSOL = 1,             ! CCN,GCCN: 0=off, 1=userset
+   IAEROSOL = 1,             ! CCN-1,CCN-2: 0=off, 1=userset
    ISALT    = 1,             ! Sea Salt: 0=off, 1=userset, 2=saltmodel
    IDUST    = 1,             ! Dust: 0=off, 1=userset 2=dustmodel
    IABCARB = 0,              ! Absorbing carbon: 0=off, 1=userset
@@ -576,8 +579,8 @@
    IAEROPRNT  = 1,           ! Print aerosol init profiles (0=no,1=yes)
    IAEROHIST  = 0,           ! Re-initialize aerosols on hist restart:0,1 
    CIN_MAX    = 0.01,        ! Ice Nuclei (#/mg)
-   CCN_MAX    = 1000.,       ! CCN (#/mg)
-   GCCN_MAX   = 0.01,        ! Giant-CCN (#/mg)
+   CCN1_MAX   = 1000.,       ! CCN-mode-1 (#/mg)
+   CCN2_MAX   = 0.01,        ! CCN-mode-2 (#/mg)
    DUST1_MAX  = 100.,        ! Small Dust Mode (#/mg)
    DUST2_MAX  = 10.,         ! Large Dust Mode (#/mg)
    SALTF_MAX  = 100.,        ! Film Sea Salt (#/mg)
@@ -593,7 +596,7 @@
    AERO_EPSILON = 0.90,0.90,0.05,0.05,1.00,1.00,1.00,0.05,0.05,0.20,0.20, 
 
    ! Aerosol 9 categories initial median radius (meters)
-   AERO_MEDRAD  = 0.04e-6,3.00e-6,          !CCN,GCCN
+   AERO_MEDRAD  = 0.04e-6,3.00e-6,          !CCN-1,CCN-2
                   0.05e-6,0.50e-6,          !Dust1,Dust2
                   0.10e-6,1.00e-6,6.00e-6,  !SeaSalt: film,jet,spume
                   0.05e-6,0.05e-6,          !Absorbing carbon

bin.rams/REVUIN.testonly bin.rams/REVUIN.testrunonlybin.rams/REVUIN.testonly renamed to bin.rams/REVUIN.testrunonly

@@ -0,0 +1,3 @@
+#!/bin/bash
+rm -f *.mod rams rams*.a
+rm -fr testrun.output

bin.rams/cleanup.sc

@@ -0,0 +1 @@
+floyd

bin.rams/machs

@@ -9,28 +9,8 @@
 #SINGLE MACHINE
 #`hostname`
 
-#Using "ccn" cluster with MPICH
-#node01:1
-#node02:8
-#node03:8
-#node04:8
-#node05:8
-#node06:8
-#node07:8
-#node08:8
-
-#Using "ccn" cluster with openMPI
-#node01 slots=1
-#node02 slots=8
-#node03 slots=8
-#node04 slots=8
-#node05 slots=8
-#node06 slots=8
-#node07 slots=8
-#node08 slots=8
-
 #Using "frost" cluster with MPICH
-#frost:1
+#frost:16
 #frost1:16
 #frost2:16
 #frost3:16
@@ -40,12 +20,18 @@
 #frost7:16
 #frost8:16
 
-#Using "ice" cluster (infiniband) MPICH
-#icehome_ib:8
-#ice1_ib:12
-#ice2_ib:12
-#ice3_ib:12
-#ice4_ib:12
+#Using "ice" cluster
+#ice:8
+#ice1:12
+#ice2:12
+#ice3:12
+#ice4:12
+
+#Using "snow" cluster
+#snow:1
+#snowfall1:64
+#snowfall2:64
+#snowfall3:64
 
 #Ciracluster (head node is cm00, but do not include that in list)
 #cc00:12

bin.rams/machs.master

@@ -8,7 +8,7 @@
 # this script in parallel or serial.
 #
 # A couple of important items here for this test simulation.
-# 1. RAMSIN.supercell - produces a 3D 1-grid supercell simulation with
+# 1. RAMSIN.testrunonly - produces a 3D 1-grid supercell simulation with
 #  LEVEL=3 microphysics
 # 2. This idealized simulation does not require geographical data (sfctypehdf5)
 #  for running since geography does not matter. Also, we do not need gridded
@@ -19,25 +19,29 @@
 #  but NOT on a supercomputer using a PBS QSUB queuing system. Consult their
 #  userguides for running parallel jobs on their systems. Each system is unique.
 # /home/smsaleeb/software/mpich-3.3.2/bin/mpiexec -machinefile machs -np 8 \
-# ./bin.rams/rams-6.3.01 -f RAMSIN.supercell
-# Note: might have to add (-ifrace eth0) to this executable statement or
+# ./bin.rams/rams-6.3.01 -f RAMSIN.testrunonly
+# Note: might have to add (-iface eth0) to this executable statement or
 #  something similar depending on how your compute nodes communicate. Use
 #  utility (ifconfig) to find out how your nodes communicate (ie. eth0 or eth1).
 #
 # Do not blindly use this script for running every simulation. It is simply
 # included here as a starting point and because I use this frequently on my
 # desktop Linux workstation for RAMS tests and debugging. If using this script
-# please become familiar with its flags, settings, and functionality. It cannot
-# be used for every runtime situation.
+# and RAMSIN namelist, please become familiar with its flags, settings, and
+# functionality. They cannot be used for every runtime situation. Many RAMSIN
+# flags in this test example are turned on for testing only and are not
+# appropriate for a real simulation to study.
 ###############################################################################
 # Set your RAMS root path
 rd=`pwd`/..
+# RAMSIN name
+ramsin="RAMSIN.testrunonly"
 # RAMS version (ie. 6.1.6)
-vs=6.3.02
+vs=6.3.04
 # Set flag for type of test (0=sequential, 1=parallel)
-runtype=0
+runtype=1
 # Set number of nodes for parallel run.
-n=10
+n=8
 # Set delete flag (0 = do not delete, 1 = delete and start over)
 del=1
 
@@ -56,8 +60,8 @@ a3=$rd/bin.rams/rams-$vs
 a4=$rd/bin.revu/revu-$vs
 
 #Check to see that RAMSIN namelist exists
-if [ ! -f $rd/bin.rams/RAMSIN.supercell ]; then
- echo "Input paths for this file is incorrect: RAMSIN.supercell"
+if [ ! -f $rd/bin.rams/$ramsin ]; then
+ echo "Input paths for this file is incorrect: RAMSIN.testrunonly"
  exit
 fi
 
@@ -92,11 +96,10 @@ fi
 # DONE WITH NECESSARY USER CHANGES
 ###############################################################################
 
-for dirname in $rd/bin.rams/test.supercell
+for dirname in $rd/bin.rams/testrun.output
 do
   if [ -d $dirname -a $del -eq 1 ]; then
-   rm -f $dirname/*.h5 $dirname/*.txt $dirname/*.tag \
-         $dirname/r.* $dirname/ct.* $dirname/out
+   rm -f $dirname/*.h5 $dirname/*.txt
   else
    if [ ! -d $dirname ]; then mkdir $dirname; fi;
   fi
@@ -114,9 +117,4 @@ else
   exit
 fi
 
-$rc1 $rd/bin.rams/RAMSIN.supercell
-
-#Try running REVU on test simulation output if REVU is compiled
-if [ -f $a4 ]; then
- $a4 -f $rd/bin.rams/REVUIN.supercell
-fi
+$rc1 $rd/bin.rams/$ramsin