Clean up code and add several minor features (CICE-Consortium#750)

* Update/improve debug_blocks output, see CICE-Consortium#718.

* Add ICE_MEMUSE cice.settings flag for batch memory use
Add set_env.memsmall, memmed, memlarge options
To use, will require changes to the env machine files.  Most machines will probably not use it.
See CICE-Consortium#674.

* Add setup_machparams.csh to compute batch/launch machine parameters
Update cice.batch.csh and cice.launch.csh to use setup_machparams.csh
See CICE-Consortium#650

* Update subroutine diagnostic_abort which calls print_state
Update ice_transport_remap and ice_transport_driver to call diagnostic_abort
  during some errors.
See also CICE-Consortium#622

* Update miniconda install information
See CICE-Consortium#547

* Code cleanup based on compile with -Wall
Code cleanup based on -std f2003 and f2008 checks
Add -stand f08 to cheyenne_intel debug flags
Add -std f2008 to cheyenne_gnu debug flags
Code consistent with Fortran 2003 except for use of contiguous in
  1d evp code.

* Remove all trailing blank space with script

* Update the cheyenne env so qc testing works
Add configuration/scripts/tests/qctest.yml file
Update documentation

* Update Icepack

* Clean up some output

* fix comments

* update print_state output

cicecore/cicedynB/analysis/ice_history_drag.F90

@@ -1,7 +1,7 @@
 !=======================================================================
 
 ! 2013 module for form drag parameters
-! authors Michel Tsamados, David Schroeder, CPOM 
+! authors Michel Tsamados, David Schroeder, CPOM
 
       module ice_history_drag
 
@@ -17,7 +17,7 @@ module ice_history_drag
       implicit none
       private
       public :: accum_hist_drag, init_hist_drag_2D
-      
+
       !---------------------------------------------------------------
       ! flags: write to output file if true or histfreq value
       !---------------------------------------------------------------
@@ -31,7 +31,7 @@ module ice_history_drag
       !---------------------------------------------------------------
 
       namelist / icefields_drag_nml /     &
-           f_Cdn_atm,        f_Cdn_ocn       , & 
+           f_Cdn_atm,        f_Cdn_ocn       , &
            f_drag
 
       !---------------------------------------------------------------
@@ -47,7 +47,7 @@ module ice_history_drag
            n_Cdn_atm_skin   , n_Cdn_atm_floe,  &
            n_Cdn_atm_pond   , n_Cdn_atm_rdg,  &
            n_Cdn_ocn_skin   , n_Cdn_ocn_floe,   &
-           n_Cdn_ocn_keel   , n_Cdn_atm_ratio    
+           n_Cdn_ocn_keel   , n_Cdn_atm_ratio
 
 !=======================================================================
 
@@ -124,43 +124,43 @@ subroutine init_hist_drag_2D
             "hdraft: draught",                           &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_hridge,"hridge","m",tstr2D, tcstr, &
             "hridge: ridge height",                          &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_distrdg,"distrdg","m",tstr2D, tcstr, &
             "distrdg: distance between ridges",  &
             "none", c1, c0,            &
-            ns, f_drag)            
+            ns, f_drag)
 
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_hkeel,"hkeel","m",tstr2D, tcstr, &
             "hkeel: keel depth",                           &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_dkeel,"dkeel","m",tstr2D, tcstr, &
             "dkeel: distance between keels", &
             "none", c1, c0,            &
-            ns, f_drag)            
+            ns, f_drag)
 
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_lfloe,"lfloe","m",tstr2D, tcstr, &
             "lfloe: floe length",         &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_dfloe,"dfloe","m",tstr2D, tcstr, &
             "dfloe: distance between floes", &
             "none", c1, c0,            &
-            ns, f_drag)   
-  
+            ns, f_drag)
+
        if (f_Cdn_atm(1:1) /= 'x') &
          call define_hist_field(n_Cdn_atm,"Cdn_atm","none",tstr2D, tcstr, &
             "Ca: total ice-atm drag coefficient", &
@@ -172,49 +172,49 @@ subroutine init_hist_drag_2D
             "Cdn_ocn: total ice-ocn drag coefficient", &
             "none", c1, c0,            &
             ns, f_Cdn_ocn)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_atm_skin,"Cdn_atm_skin","none", &
             tstr2D, tcstr, &
             "Cdn_atm_skin: neutral skin ice-atm drag coefficient", &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_atm_floe,"Cdn_atm_floe","none", &
             tstr2D, tcstr, &
             "Cdn_atm_floe: neutral floe edge ice-atm drag coefficient", &
             "none", c1, c0,            &
-            ns, f_drag)            
- 
+            ns, f_drag)
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_atm_pond,"Cdn_atm_pond","none", &
             tstr2D, tcstr, &
             "Cdn_atm_pond: neutral pond edge ice-atm drag coefficient", &
             "none", c1, c0,            &
             ns, f_drag)
-            
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_atm_rdg,"Cdn_atm_rdg","none", &
             tstr2D, tcstr, &
             "Cdn_atm_rdg: neutral ridge ice-atm drag coefficient", &
             "none", c1, c0,            &
             ns, f_drag)
-            
+
         if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_ocn_skin,"Cdn_ocn_skin","none", &
             tstr2D, tcstr, &
             "Cdn_ocn_skin: neutral skin ice-ocn drag coefficient", &
             "none", c1, c0,            &
             ns, f_drag)
- 
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_ocn_floe,"Cdn_ocn_floe","none", &
             tstr2D, tcstr, &
             "Cdn_ocn_floe: neutral floe edge ice-ocn drag coefficient", &
             "none", c1, c0,            &
-            ns, f_drag)            
- 
+            ns, f_drag)
+
        if (f_drag(1:1) /= 'x') &
          call define_hist_field(n_Cdn_ocn_keel,"Cdn_ocn_keel","none", &
             tstr2D, tcstr, &
@@ -281,21 +281,21 @@ subroutine accum_hist_drag (iblk)
         call accum_hist_field(n_lfloe, iblk, lfloe(:,:,iblk), a2D)
         call accum_hist_field(n_dfloe, iblk, dfloe(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_atm_rdg, &
-                              iblk, Cdn_atm_rdg(:,:,iblk), a2D)   
+                              iblk, Cdn_atm_rdg(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_atm_floe, &
                               iblk, Cdn_atm_floe(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_atm_pond, &
                               iblk, Cdn_atm_pond(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_atm_skin, &
-                              iblk, Cdn_atm_skin(:,:,iblk), a2D)   
+                              iblk, Cdn_atm_skin(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_atm_ratio, &
                               iblk, Cdn_atm_ratio(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_ocn_keel, &
-                              iblk, Cdn_ocn_keel(:,:,iblk), a2D)  
+                              iblk, Cdn_ocn_keel(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_ocn_floe, &
                               iblk, Cdn_ocn_floe(:,:,iblk), a2D)
         call accum_hist_field(n_Cdn_ocn_skin, &
-                              iblk, Cdn_ocn_skin(:,:,iblk), a2D)  
+                              iblk, Cdn_ocn_skin(:,:,iblk), a2D)
       end if
 
       endif ! if(allocated(a2D))

cicecore/cicedynB/analysis/ice_history_fsd.F90

@@ -21,7 +21,7 @@ module ice_history_fsd
       private
       public :: accum_hist_fsd, init_hist_fsd_2D, init_hist_fsd_3Df, &
                 init_hist_fsd_4Df
-      
+
       !---------------------------------------------------------------
       ! flags: write to output file if true or histfreq value
       !---------------------------------------------------------------
@@ -79,7 +79,6 @@ subroutine init_hist_fsd_2D
 
       integer (kind=int_kind) :: ns
       integer (kind=int_kind) :: nml_error ! namelist i/o error flag
-      real    (kind=dbl_kind) :: secday
       logical (kind=log_kind) :: tr_fsd, wave_spec
 
       character(len=*), parameter :: subname = '(init_hist_fsd_2D)'
@@ -273,12 +272,12 @@ subroutine init_hist_fsd_4Df
          if (histfreq(ns) /= 'x') then
 
          if (f_afsdn(1:1) /= 'x') &
-            call define_hist_field(n_afsdn,"afsdn","1",tstr4Df, tcstr, & 
+            call define_hist_field(n_afsdn,"afsdn","1",tstr4Df, tcstr, &
                "areal floe size and thickness distribution",    &
                "per unit bin width", c1, c0, ns, f_afsdn)
 
          endif ! if (histfreq(ns) /= 'x') then
-      enddo ! ns 
+      enddo ! ns
 
       endif ! tr_fsd
 
@@ -398,7 +397,7 @@ subroutine accum_hist_fsd (iblk)
       if (f_fsdrad(1:1) /= 'x') then
          do j = 1, ny_block
          do i = 1, nx_block
-            worka(i,j) = c0            
+            worka(i,j) = c0
             if (aice_init(i,j,iblk) > puny) then
              do k = 1, nfsd_hist
                 do n = 1, ncat_hist
@@ -450,7 +449,7 @@ subroutine accum_hist_fsd (iblk)
          end do
          call accum_hist_field(n_afsd-n3Dacum, iblk, nfsd_hist, worke, a3Df)
       endif
- 
+
       if (f_dafsd_newi(1:1)/= 'x') &
              call accum_hist_field(n_dafsd_newi-n3Dacum, iblk, nfsd_hist, &
                                     d_afsd_newi(:,:,1:nfsd_hist,iblk), a3Df)
@@ -473,7 +472,7 @@ subroutine accum_hist_fsd (iblk)
 
       if (f_afsdn(1:1) /= 'x') then
          do n = 1, ncat_hist
-         do k = 1, nfsd_hist 
+         do k = 1, nfsd_hist
          do j = 1, ny_block
          do i = 1, nx_block
             workd(i,j,k,n) = trcrn(i,j,nt_fsd+k-1,n,iblk) &

cicecore/cicedynB/analysis/ice_history_mechred.F90

@@ -20,7 +20,7 @@ module ice_history_mechred
       implicit none
       private
       public :: accum_hist_mechred, init_hist_mechred_2D, init_hist_mechred_3Dc
-      
+
       !---------------------------------------------------------------
       ! flags: write to output file if true or histfreq value
       !---------------------------------------------------------------
@@ -188,13 +188,13 @@ subroutine init_hist_mechred_2D
              "ice area ridging rate",                                      &
              "none", secday*c100, c0,                                      &
              ns, f_dardg1dt)
-      
+
       if (f_dardg2dt(1:1) /= 'x') &
          call define_hist_field(n_dardg2dt,"dardg2dt","%/day",tstr2D, tcstr, &
              "ridge area formation rate",                                  &
              "none", secday*c100, c0,                                      &
              ns, f_dardg2dt)
-      
+
       if (f_dvirdgdt(1:1) /= 'x') &
          call define_hist_field(n_dvirdgdt,"dvirdgdt","cm/day",tstr2D, tcstr, &
              "ice volume ridging rate",                                     &

cicecore/cicedynB/analysis/ice_history_pond.F90

@@ -20,7 +20,7 @@ module ice_history_pond
       implicit none
       private
       public :: accum_hist_pond, init_hist_pond_2D, init_hist_pond_3Dc
-      
+
       !---------------------------------------------------------------
       ! flags: write to output file if true or histfreq value
       !---------------------------------------------------------------
@@ -40,17 +40,17 @@ module ice_history_pond
       namelist / icefields_pond_nml /     &
            f_apondn,    f_apeffn   , &
            f_hpondn,                 &
-           f_apond,     f_apond_ai , &  
-           f_hpond,     f_hpond_ai , &  
-           f_ipond,     f_ipond_ai , &  
+           f_apond,     f_apond_ai , &
+           f_hpond,     f_hpond_ai , &
+           f_ipond,     f_ipond_ai , &
            f_apeff,     f_apeff_ai
 
       !---------------------------------------------------------------
       ! field indices
       !---------------------------------------------------------------
 
       integer (kind=int_kind), dimension(max_nstrm) :: &
-           n_apondn      , n_apeffn    , & 
+           n_apondn      , n_apeffn    , &
            n_hpondn      , &
            n_apond       , n_apond_ai, &
            n_hpond       , n_hpond_ai, &
@@ -147,7 +147,7 @@ subroutine init_hist_pond_2D
              ns, f_apond)
 
       if (f_apond_ai(1:1) /= 'x') &
-         call define_hist_field(n_apond_ai,"apond_ai","1",tstr2D, tcstr, & 
+         call define_hist_field(n_apond_ai,"apond_ai","1",tstr2D, tcstr, &
              "melt pond fraction of grid cell",                    &
              "weighted by ice area", c1, c0,                       &
              ns, f_apond_ai)
@@ -159,7 +159,7 @@ subroutine init_hist_pond_2D
              ns, f_hpond)
 
       if (f_hpond_ai(1:1) /= 'x') &
-         call define_hist_field(n_hpond_ai,"hpond_ai","m",tstr2D, tcstr, & 
+         call define_hist_field(n_hpond_ai,"hpond_ai","m",tstr2D, tcstr, &
              "mean melt pond depth over grid cell",                &
              "weighted by ice area", c1, c0,                       &
              ns, f_hpond)
@@ -171,7 +171,7 @@ subroutine init_hist_pond_2D
              ns, f_ipond)
 
       if (f_ipond_ai(1:1) /= 'x') &
-         call define_hist_field(n_ipond_ai,"ipond_ai","m",tstr2D, tcstr, & 
+         call define_hist_field(n_ipond_ai,"ipond_ai","m",tstr2D, tcstr, &
              "mean pond ice thickness over grid cell",             &
              "weighted by ice area", c1, c0,                       &
              ns, f_ipond_ai)
@@ -192,7 +192,7 @@ subroutine init_hist_pond_2D
       enddo ! nstreams
 
       endif ! tr_pond
-      
+
       end subroutine init_hist_pond_2D
 
 !=======================================================================
@@ -212,14 +212,14 @@ subroutine init_hist_pond_3Dc
          file=__FILE__, line=__LINE__)
 
       if (tr_pond) then
-      
+
       ! 3D (category) variables must be looped separately
       do ns = 1, nstreams
         if (histfreq(ns) /= 'x') then
 
         if (f_apondn(1:1) /= 'x') &
            call define_hist_field(n_apondn,"apondn","1",tstr3Dc, tcstr, &
-              "melt pond fraction, category","none", c1, c0,      &            
+              "melt pond fraction, category","none", c1, c0,      &
               ns, f_apondn)
 
         if (f_hpondn(1:1) /= 'x') &
@@ -376,7 +376,7 @@ subroutine accum_hist_pond (iblk)
                                                   * trcr(:,:,nt_ipnd,iblk), a2D)
          endif ! ponds
 
-         this_block = get_block(blocks_ice(iblk),iblk)         
+         this_block = get_block(blocks_ice(iblk),iblk)
          ilo = this_block%ilo
          ihi = this_block%ihi
          jlo = this_block%jlo