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LaGriT/docs/pages/release_notes/lagrit_release_notes_V3.100.md
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LaGriT Release Notes V3.1

LaGriT V3.108 July 2016

The was the Last version released under Open Distribution license LA-CC-2012-084 before Open Source.

This code was tagged in Mercurial as V3.108 and used to start open-source repository on github.

This includes work by summer student Mikita Yankouski with WIN development using Cygwin.

  • Added top level python control suite, and standarized level02 output files. See instructions.txt and cmake-script.
  • Files changed for WIN are opsys.h and type_sizes.h to account for win64 and changed define for SIZEOF_LONG
file: opsys.h
#ifdef win64
 #define FCV_UNDERSCORE
 #define SIZEOF_INT 4
 #define SIZEOF_LONG 8
 #define SIZEOF_VOIDP 8
 #define MAX_UINT 18446744073709551615.00 
#endif
         
#ifdef win64
 #define int_ptrsize long long

file: type_sizes.h
#ifdef __CYGWIN__
 #define FCV_UNDERSCORE
 #define SIZEOF_INT 4
 #define SIZEOF_LONG 4
 #define SIZEOF_VOIDP 8
#endif 

file: machine_header.h
#ifdef win64
 #define FCV_UNDERSCORE
 #define SIZEOF_INT 4
 #define SIZEOF_LONG 8
 #define SIZEOF_VOIDP 8
#endif

file: Makefile
ifeq ($(COMPILER), cygwin)
  SUFFC = _cygwin
  FC = /bin/gfortran
  CC = /bin/gcc
  CXX = /bin/c++
  FC90 = /bin/gfortran
  OSTAG = _cygwin
         
 FFLAGS = -fcray-pointer -fdefault-integer-8 -m64 -Dwin64
 FF90FLAGS = -fcray-pointer -fdefault-integer-8 -m64 -Dwin64
 CFLAGS = -m64 -Dwin64

LaGriT V3.106 August 2015

Major update to write PFLOTRAN type option stor file and new syntax using Exodus II 6.9 libraries.

Note: The LaGriT run-time banner shows V3.2 with compile date Aug 2015, even though it is actually a branch from V3.106.

Enhancements:

  • dump / pflotran Writes .uge file for pflotran and is used by the DFN suite of scripts. The deve directory is in /n/swdev/LAGRIT/work/pflotran. The syntax looks like:
   dump / pflotran / root_name / cmo_name
   dump / pflotran / root_name / cmo_name / nofilter_zero
  • dump / exo calls ExodusII new routines changed from V5 to V6. LaGriT command syntax is unchanged.
           http://sourceforge.net/projects/exodusii/files/
           Exodus II 6.09
           HDF5 version 1.8.6
           netcdf-4.1.3
  • exo block id modified to input digit instead of digit0000. All exodus files are same as Exodus II 5, except for the block id. Tests have been updated resulting in the following differences:
        Exodus 6.09:
        <               :api_version = 6.09f ;
        <               :version = 6.09f ;
        ---
        <  eb_prop1 = 1, 2, 3 ;

        Exodus 5.22a:
                       :api_version = 5.22f ;
                       :version = 5.22f ;
        ---
          eb_prop1 = 10000, 20000, 30000 ;
  • compress_eps new cmo attribute for stor file allowing user to extend range of ccoef values by setting mesh attribute compress_eps (from default 1e-8). Changing value of compress_epsilon seemed to help loss of coeffs with large aspect ratios.

These issues were fixed:

  • dump / stor corrected bug for 2D grids that overwrite volic with incorrect value if grid is non-planer.

  • dump / fehm add space between ns and nelements, increase to i12

  • read / fehm fixed seg fault for 0 elem report message by using a,a instead of a in write format.

  • build ExodusII6 libraries The following issue was fixed when building static libraries with exodus:

These are the external libs used with LaGriT V3.1 As of November 2012
         http://sourceforge.net/projects/exodusii/files/
         Exodus II 5.22a
         HDF5 version 1.8.6
         netcdf-4.1.3
         
Error in Library inclusion order in the following places:
        1. /n/swdev/src/exodusii/exodus-6.09/exodus/cbind/CMakeList.txt 
            Line 284
        2. /n/swdev/src/exodusoo/exodus-6.09/exodus/forbind/CMakeList.txt
            Line 62
            
Solution was to switch ${HDF5_LIBRARY with ${HDF5HL_LIBRARY
    
Linux RHEL Exodus 5 libraries were built in /n/swdev/LAGRIT/VERS_3.100_012_NOV09/build_lagrit/exodus

Build executable for linux:
gfortran -O -Dlinx64 -static -fcray-pointer -fdefault-integer-8 -fno-sign-zero -o mylagrit lagrit_main.o lagrit_fdate.o lagrit_lin64_o_gf4.5.a /n/swdev/LAGRIT/VERS_3.100_012_NOV09/build_lagrit/lg_util/lib/util_lin64_o_gfort4.5.a -L /n/swdev/LAGRIT/VERS_3.100_012_NOV09/build_lagrit/exodus/lin64/lib -lexoIIv2for -lexodus -lnetcdf -lhdf5_hl -lhdf5 -lz -lm -lstdc++

LaGriT V3.101 November 2013

Note for DFNWorks applications using LaGriT, this version does NOT have the PFLOTRAN file option. This version of code uses ExodusII 5 routine calls. These are replaced with ExodusII 6 in newer versions.

V3.103 is last version lagrit code using Exodus 5 libs

V3.104 is new version lagrit code using Exodus 6 libs

Enhancements:

  • read / zone or zone_element added option zone_element which allows reading of node or element list in FEHM zone or zonn format. Each node or element number found in the list has attribute tagged.

These issues were fixed:

  • addatt/mo_tri / unit_area_normal fixed incorrect zero result and fixed attribute handling so vector array is formed using irank = 3.

  • cmo/addatt/ mo/ area_normal/xyz/ Result is off by factor of 2, fixed area normal to assign half the cross product (for triangles).

  • synth_norm fixed handling of attributes. The synthetic normals were creating a dummy attribute not used because offsetsurf is creating x_n_norm y_n_norm z_n_norm on the input cmo. Attribute names are ignored on the command line, added better reporting for this.

LaGriT V3.100 November 2012

Major changes to most parts of the code to enable 64 bit compilation and added external ExodusII 5 libraries to write Exodus basic mesh files. This includes work by Quan Bui for ExodusII node sets and element sets.

Enhancements:

  • dump / exo Now includes netcdf and exodus libs for writing exodus mesh files and reading and writing facesets.
        Syntax:
          dump / exo / ifile / cmoname

          Dump exodus files with/without facesets, fast/slow options:
          dump / exo / ifile / cmoname / facesets / on
          dump / exo / ifile / cmoname / facesets / off
          dump / exo / ifile / cmoname / facesets / on file1,file2,...filen
          dump / exo / ifile / cmoname / facesets / off file1,file2,...filen

          write exo pset and eltsets:
          dump / exo / filenam.exo / cmoname / psets / eltsets /
          dump/exo/mesh_07.exo/mo7//eltsets/ &
             facesets bc01.faceset &
             bc02.faceset bc03.faceset bc04.faceset &
             bc05.faceset bc08.faceset bc09.faceset
          dump/exo/mesh_06.exo/mo6/psets// &
             facesets bc01.faceset &
             bc02.faceset bc03.faceset bc04.faceset &
             bc05.faceset bc08.faceset bc09.faceset

  • dump 3 token short syntax for dump (avs,gmv,lg,lagrit,ts,exo)

  • extract/surfmesh Now creates attributes to hold element local face numbers of 3D input mesh that occur on either side of output mesh face, idface0 and idface1. Now copies user-created node-based attributes from source.

  • interpolate Changed interpolate to "find" more points on edges this will permit nodes to find a nearest edge or point and be "inside" the triangle for extreme small or large numbers where epsilon values are difficult to evaluate correctly.

  • massage Added option for massage to refine based on an attribute field.

  Syntax:
          massage / [bisection length/field name] / merge_length / toldamage / ...
  • massage2 Under development massage2 syntax for incremental refinement strategies.
  Syntax:
          massage2/ [file name] / [Target Length Scale]/[field name]/ &
             merge_length/toldamage/[tolroughness]/[ifirst,ilast,istride]/ ...

  • math add modulo and mod options

  • recon Code improvements related to recon 0 and recon 1 will result in slightly different but better connectivity results.

  • sort Added line sort by nodes or elements for creating valid polygons that can be read and used by other routines.

   Syntax:
          sort / line_graph / cmo / ascending  descending / [key] / [nodes/elements]

These issues were fixed:

  • cmo/copyatt fix copy from node attribute to elem attribute of equal length

  • cmo/readatt fix to allow character in first position which will be skipped

  • minor fixes related to 64 bit code changes. Improved error catching for common routines.

Changesets tracked in Mercurial/Trac on ancho.lanl.gov/lagrit

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