[Dart-dev] [3233] DART/trunk: Major update to merge_obs_seq:

nancy at subversion.ucar.edu nancy at subversion.ucar.edu
Wed Feb 13 10:08:08 MST 2008


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Copied: DART/trunk/models/lorenz_96/tests (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests)

Deleted: DART/trunk/models/lorenz_96/tests/README
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/README	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/README	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,20 +0,0 @@
-
-
-The test_merge.ksh script is a self-contained script
-that constructs input.nml files and runs merge_obs_seq.
-
-It prints out the test number and output from the run
-into a log file, and if the output sequence file is short,
-concatenates the entire output file in the log; if it's long,
-it prints out the first and last 30 values.
-
-If the test is expected to fail, it has a 'fail' keyword
-in the test.   This does test various overlaps of files
-and start/stop times, but the checking is far from automated
-and it doesn't test a few other things which need testing
-like squeezing out unused obs or sorting (which it does but
-there's just no specific test for it yet).
-
-nancy
-12.feb.2008
-

Copied: DART/trunk/models/lorenz_96/tests/README (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/README)
===================================================================
--- DART/trunk/models/lorenz_96/tests/README	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/README	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,20 @@
+
+
+The test_merge.ksh script is a self-contained script
+that constructs input.nml files and runs merge_obs_seq.
+
+It prints out the test number and output from the run
+into a log file, and if the output sequence file is short,
+concatenates the entire output file in the log; if it's long,
+it prints out the first and last 30 values.
+
+If the test is expected to fail, it has a 'fail' keyword
+in the test.   This does test various overlaps of files
+and start/stop times, but the checking is far from automated
+and it doesn't test a few other things which need testing
+like squeezing out unused obs or sorting (which it does but
+there's just no specific test for it yet).
+
+nancy
+12.feb.2008
+

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.A
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.A	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.A	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,35 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            2  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Quality Control                                                                                                                  
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.A (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.A)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.A	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.A	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,35 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            2  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Quality Control                                                                                                                  
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.B
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.B	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.B	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,38 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            2  num_qc:            2
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Quality Control                                                                                                                  
-Quality Control 2                                                                                                                
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.B (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.B)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.B	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.B	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,38 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            2  num_qc:            2
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Quality Control                                                                                                                  
+Quality Control 2                                                                                                                
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.C
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.C	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.C	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,35 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            2  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Special Quality Control                                                                                                           
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.C (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.C)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.C	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.C	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,35 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            2  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Special Quality Control                                                                                                           
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.D
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.D	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.D	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,38 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            3  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-second copy of truth                                                                                                             
-Quality Control                                                                                                                  
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.D (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.D)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.D	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.D	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,38 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            3  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+second copy of truth                                                                                                             
+Quality Control                                                                                                                  
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.E
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.E	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.E	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,34 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           1
-           1 RAW_STATE_VARIABLE              
-  num_copies:            2  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Quality Control                                                                                                                  
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.E (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.E)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.E	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.E	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,34 @@
+ obs_sequence
+obs_kind_definitions
+           1
+           1 RAW_STATE_VARIABLE              
+  num_copies:            2  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Quality Control                                                                                                                  
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.F
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.F	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.F	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,35 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RADIOSONDE_TEMPERATURE
-  num_copies:            2  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Quality Control                                                                                                                  
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3600          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  3600          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.F (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.F)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.F	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.F	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,35 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RADIOSONDE_TEMPERATURE
+  num_copies:            2  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Quality Control                                                                                                                  
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  3600          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  3600          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.G
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.G	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.G	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,35 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            2  num_qc:            1
-  num_obs:          2  max_num_obs:            2
-observations                                                                                                                     
-truth                                                                                                                            
-Quality Control                                                                                                                  
-  first:            1  last:        2
- OBS            1
-   2.33136633410425     
-   3.47889361011565     
-   0.00000000000000     
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  7200          0
-   1.00000000000000     
- OBS            2
-   4.40993275557209     
-   4.79362930462177     
-   0.00000000000000     
-           1           -1          -1
-obdef
-loc1d
-  0.171148413632676     
-kind
-           1
-  7200          0
-   1.00000000000000     

Copied: DART/trunk/models/lorenz_96/tests/obs_seq.G (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.G)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.G	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.G	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,35 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            2  num_qc:            1
+  num_obs:          2  max_num_obs:            2
+observations                                                                                                                     
+truth                                                                                                                            
+Quality Control                                                                                                                  
+  first:            1  last:        2
+ OBS            1
+   2.33136633410425     
+   3.47889361011565     
+   0.00000000000000     
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+  7200          0
+   1.00000000000000     
+ OBS            2
+   4.40993275557209     
+   4.79362930462177     
+   0.00000000000000     
+           1           -1          -1
+obdef
+loc1d
+  0.171148413632676     
+kind
+           1
+  7200          0
+   1.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.L
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.L	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.L	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,557 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
-  num_obs:           61  max_num_obs:           61
-  first:            1  last:           61
- OBS            1
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3601          0
-   2.00000000000000     
- OBS            2
-           1           3          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3661          0
-   2.00000000000000     
- OBS            3
-           2           4          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3721          0
-   2.00000000000000     
- OBS            4
-           3           5          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3781          0
-   2.00000000000000     
- OBS            5
-           4           6          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
-  3841          0
-   2.00000000000000     
- OBS            6
-           5           7          -1
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.L (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.L)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.L	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.L	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,557 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           61  max_num_obs:           61
+  first:            1  last:           61
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Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.M
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.M	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.M	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,557 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
-  num_obs:           61  max_num_obs:           61
-  first:            1  last:           61
- OBS            1
-          -1           2          -1
-obdef
-loc1d
-  0.390042510120342     
-kind
-           1
- 10801          0
-   2.00000000000000     
- OBS            2
-           1           3          -1
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-  0.390042510120342     
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-           1
- 10861          0
-   2.00000000000000     
- OBS            3
-           2           4          -1
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-  0.390042510120342     
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-           1
- 10921          0
-   2.00000000000000     
- OBS            4
-           3           5          -1
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-  0.390042510120342     
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-           1
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-           4           6          -1
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.M (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.M)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.M	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.M	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,557 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           61  max_num_obs:           61
+  first:            1  last:           61
+ OBS            1
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 10801          0
+   2.00000000000000     
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+           1           3          -1
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+  0.390042510120342     
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+           1
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+   2.00000000000000     
+ OBS            3
+           2           4          -1
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+  0.390042510120342     
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+           1
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+   2.00000000000000     
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+           3           5          -1
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+           1
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+          56          58          -1
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+  0.390042510120342     
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+           1
+ 14161          0
+   2.00000000000000     
+ OBS           58
+          57          59          -1
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+  0.390042510120342     
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+           1
+ 14221          0
+   2.00000000000000     
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+          58          60          -1
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+           1
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+          59          61          -1
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+           1
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+   2.00000000000000     
+ OBS           61
+          60          -1          -1
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+  0.390042510120342     
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+           1
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+   2.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.N
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.N	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.N	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,557 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
-  num_obs:           61  max_num_obs:           61
-  first:            1  last:           61
- OBS            1
-          -1           2          -1
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-loc1d
-  0.390042510120342     
-kind
-           1
- 18001          0
-   2.00000000000000     
- OBS            2
-           1           3          -1
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-  0.390042510120342     
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-           1
- 18061          0
-   2.00000000000000     
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-           2           4          -1
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-  0.390042510120342     
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-           1
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-   2.00000000000000     
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-           3           5          -1
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-           4           6          -1
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.N (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.N)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.N	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.N	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,557 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           61  max_num_obs:           61
+  first:            1  last:           61
+ OBS            1
+          -1           2          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18001          0
+   2.00000000000000     
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+           1           3          -1
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+  0.390042510120342     
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+           1
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+   2.00000000000000     
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+           2           4          -1
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+  0.390042510120342     
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+           1
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+   2.00000000000000     
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+           3           5          -1
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+           1
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+           4           6          -1
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Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.O
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.O	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.O	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,827 +0,0 @@
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-obs_kind_definitions
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-           2 RAW_STATE_1D_INTEGRAL           
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.O (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.O)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.O	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.O	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,827 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           91  max_num_obs:           91
+  first:            1  last:           91
+ OBS            1
+          -1           2          -1
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Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.P
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.P	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.P	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,737 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
-  num_obs:           81  max_num_obs:           81
-  first:            1  last:           81
- OBS            1
-          -1           2          -1
-obdef
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-  0.390042510120342     
-kind
-           1
-  7201          0
-   2.00000000000000     
- OBS            2
-           1           3          -1
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-  0.390042510120342     
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-           1
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-   2.00000000000000     
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-           2           4          -1
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-           1
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-   2.00000000000000     
- OBS            4
-           3           5          -1
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-           1
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-   2.00000000000000     
- OBS            5
-           4           6          -1
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.P (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.P)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.P	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.P	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,737 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           81  max_num_obs:           81
+  first:            1  last:           81
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+           1
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Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.Q
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.Q	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.Q	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,737 +0,0 @@
- obs_sequence
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-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.Q (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.Q)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.Q	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.Q	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,737 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:           81  max_num_obs:           81
+  first:            1  last:           81
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Deleted: DART/trunk/models/lorenz_96/tests/obs_seq.R
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.R	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.R	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,1097 +0,0 @@
- obs_sequence
-obs_kind_definitions
-           2
-           1 RAW_STATE_VARIABLE              
-           2 RAW_STATE_1D_INTEGRAL           
-  num_copies:            0  num_qc:            0
-  num_obs:          121  max_num_obs:          121
-  first:            1  last:          121
- OBS            1
-          -1           2          -1
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-  0.390042510120342     
-kind
-           1
- 14401          0
-   2.00000000000000     
- OBS            2
-           1           3          -1
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-           1
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-   2.00000000000000     
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-           3           5          -1
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-           4           6          -1
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Copied: DART/trunk/models/lorenz_96/tests/obs_seq.R (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/obs_seq.R)
===================================================================
--- DART/trunk/models/lorenz_96/tests/obs_seq.R	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/obs_seq.R	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,1097 @@
+ obs_sequence
+obs_kind_definitions
+           2
+           1 RAW_STATE_VARIABLE              
+           2 RAW_STATE_1D_INTEGRAL           
+  num_copies:            0  num_qc:            0
+  num_obs:          121  max_num_obs:          121
+  first:            1  last:          121
+ OBS            1
+          -1           2          -1
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+          72          74          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18721          0
+   2.00000000000000     
+ OBS           74
+          73          75          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18781          0
+   2.00000000000000     
+ OBS           75
+          74          76          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18841          0
+   2.00000000000000     
+ OBS           76
+          75          77          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18901          0
+   2.00000000000000     
+ OBS           77
+          76          78          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 18961          0
+   2.00000000000000     
+ OBS           78
+          77          79          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19021          0
+   2.00000000000000     
+ OBS           79
+          78          80          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19081          0
+   2.00000000000000     
+ OBS           80
+          79          81          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19141          0
+   2.00000000000000     
+ OBS           81
+          80          82          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19201          0
+   2.00000000000000     
+ OBS           82
+          81          83          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19261          0
+   2.00000000000000     
+ OBS           83
+          82          84          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19321          0
+   2.00000000000000     
+ OBS           84
+          83          85          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19381          0
+   2.00000000000000     
+ OBS           85
+          84          86          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19441          0
+   2.00000000000000     
+ OBS           86
+          85          87          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19501          0
+   2.00000000000000     
+ OBS           87
+          86          88          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19561          0
+   2.00000000000000     
+ OBS           88
+          87          89          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19621          0
+   2.00000000000000     
+ OBS           89
+          88          90          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19681          0
+   2.00000000000000     
+ OBS           90
+          89          91          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19741          0
+   2.00000000000000     
+ OBS           91
+          90          92          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19801          0
+   2.00000000000000     
+ OBS           92
+          91          93          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19861          0
+   2.00000000000000     
+ OBS           93
+          92          94          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19921          0
+   2.00000000000000     
+ OBS           94
+          93          95          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 19981          0
+   2.00000000000000     
+ OBS           95
+          94          96          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20041          0
+   2.00000000000000     
+ OBS           96
+          95          97          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20101          0
+   2.00000000000000     
+ OBS           97
+          96          98          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20161          0
+   2.00000000000000     
+ OBS           98
+          97          99          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20221          0
+   2.00000000000000     
+ OBS           99
+          98         100          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20281          0
+   2.00000000000000     
+ OBS          100
+          99         101          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20341          0
+   2.00000000000000     
+ OBS          101
+         100         102          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20401          0
+   2.00000000000000     
+ OBS          102
+         101         103          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20461          0
+   2.00000000000000     
+ OBS          103
+         102         104          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20521          0
+   2.00000000000000     
+ OBS          104
+         103         105          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20581          0
+   2.00000000000000     
+ OBS          105
+         104         106          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20641          0
+   2.00000000000000     
+ OBS          106
+         105         107          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20701          0
+   2.00000000000000     
+ OBS          107
+         106         108          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20761          0
+   2.00000000000000     
+ OBS          108
+         107         109          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20821          0
+   2.00000000000000     
+ OBS          109
+         108         110          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20881          0
+   2.00000000000000     
+ OBS          110
+         109         111          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 20941          0
+   2.00000000000000     
+ OBS          111
+         110         112          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21001          0
+   2.00000000000000     
+ OBS          112
+         111         113          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21061          0
+   2.00000000000000     
+ OBS          113
+         112         114          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21121          0
+   2.00000000000000     
+ OBS          114
+         113         115          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21181          0
+   2.00000000000000     
+ OBS          115
+         114         116          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21241          0
+   2.00000000000000     
+ OBS          116
+         115         117          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21301          0
+   2.00000000000000     
+ OBS          117
+         116         118          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21361          0
+   2.00000000000000     
+ OBS          118
+         117         119          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21421          0
+   2.00000000000000     
+ OBS          119
+         118         120          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21481          0
+   2.00000000000000     
+ OBS          120
+         119         121          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21541          0
+   2.00000000000000     
+ OBS          121
+         120          -1          -1
+obdef
+loc1d
+  0.390042510120342     
+kind
+           1
+ 21601          0
+   2.00000000000000     

Deleted: DART/trunk/models/lorenz_96/tests/test_merge.ksh
===================================================================
--- DART/branches/nancy_work/models/lorenz_96/tests/test_merge.ksh	2008-02-12 23:25:31 UTC (rev 3231)
+++ DART/trunk/models/lorenz_96/tests/test_merge.ksh	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,387 +0,0 @@
-#!/bin/ksh 
-
-# test suite for merge_obs_sequence utility
-
-# set up constant part at beginning
-cat > input.nml.head <<EOF
-&obs_sequence_nml
-   write_binary_obs_sequence = .false.  /
-
-&obs_kind_nml
-   assimilate_these_obs_types = 'RAW_STATE_VARIABLE'  /
-
-&utilities_nml
-   TERMLEVEL = 1,
-   module_details = .false.,
-   logfilename = 'dart_log.out'  /
-
-
-EOF
-
-# we will concatinate onto the end of this file
-rm -fr test_merge.log
-
-# should have a second arg - expects it to fail or not
-
-# set up functions which will be used for the rest of the script
-# shortone cats the entire result into the log, longone heads the
-# first 30 and last 30 lines
-function shortone
-{
-   rm -f input.nml
-   cat input.nml.head input.fragment > input.nml
-   echo "" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo " test $1 " >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo "" >> test_merge.log
-   cat input.fragment >> test_merge.log
-   echo "" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   rm -f obs_seq.merged
-   ./merge_obs_seq 2>&1 >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   if [[ -f obs_seq.merged ]]; then
-     cat obs_seq.merged >> test_merge.log
-   else
-     echo obs_seq.merged not found  >> test_merge.log
-   fi
-}
-
-function longone
-{
-   rm -f input.nml
-   cat input.nml.head input.fragment > input.nml
-   echo "" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo " test $1 " >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   echo "" >> test_merge.log
-   cat input.fragment >> test_merge.log
-   echo "" >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   rm -f obs_seq.merged
-   ./merge_obs_seq 2>&1 >> test_merge.log
-   echo "-------------------------" >> test_merge.log
-   if [[ -f obs_seq.merged ]]; then
-     head -30 obs_seq.merged >> test_merge.log
-     echo '-------------------------' >> test_merge.log
-     tail -30 obs_seq.merged >> test_merge.log
-     echo '-------------------------' >> test_merge.log
-   else
-     echo obs_seq.merged not found  >> test_merge.log
-   fi
-}
-
-###############################
-cat - > input.fragment <<EOF
-
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.A',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = -1,
-   first_obs_seconds        = -1,
-   last_obs_days            = -1,
-   last_obs_seconds         = -1,
-  /
-
-EOF
-shortone with_self works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.A',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone with_self_no_times works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 1,
-   filename_seq    = 'obs_seq.A',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = -1,
-   first_obs_seconds        = -1,
-   last_obs_days            = -1,
-   last_obs_seconds         = -1,
-  /
-EOF
-
-shortone self_only works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.B',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_fail fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.C',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_fail fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.D',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_fail fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.E',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_fail fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.F',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_fail fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 2,
-   filename_seq    = 'obs_seq.A', 'obs_seq.G',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-shortone should_work works
-
-
-###############################
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-  /
-EOF
-
-longone case_0 works
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 0,
-   last_obs_days            = 0,
-   last_obs_seconds         = 4000,
-  /
-EOF
-
-longone case_1 works
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 7000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 11000,
-  /
-EOF
-
-longone case_2 works
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 20000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 25000,
-  /
-EOF
-
-longone case_3 works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 15000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 16000,
-  /
-EOF
-
-longone case_4 fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 0,
-   last_obs_days            = 0,
-   last_obs_seconds         = 2000,
-  /
-EOF
-
-longone case_5 fails
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 3,
-   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 25000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 28000,
-  /
-EOF
-
-longone case_6 fails
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 0,
-   last_obs_days            = 0,
-   last_obs_seconds         = 10000,
-  /
-EOF
-
-longone case_7 works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 13000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 25000,
-  /
-EOF
-
-longone case_8 works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 4000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 7000,
-  /
-EOF
-
-longone case_9 works
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 7200,
-   last_obs_days            = 0,
-   last_obs_seconds         = 9000,
-  /
-EOF
-
-longone case_9a works
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 10000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 11000,
-  /
-EOF
-
-longone case_9b works
-
-
-###############################
-cat > input.fragment <<EOF
-&merge_obs_seq_nml
-   num_input_files = 4,
-   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
-   filename_out    = 'obs_seq.merged',
-   first_obs_days           = 0,
-   first_obs_seconds        = 10000,
-   last_obs_days            = 0,
-   last_obs_seconds         = 18000,
-  /
-EOF
-
-longone case_10 works
-
-

Copied: DART/trunk/models/lorenz_96/tests/test_merge.ksh (from rev 3231, DART/branches/nancy_work/models/lorenz_96/tests/test_merge.ksh)
===================================================================
--- DART/trunk/models/lorenz_96/tests/test_merge.ksh	                        (rev 0)
+++ DART/trunk/models/lorenz_96/tests/test_merge.ksh	2008-02-13 17:08:08 UTC (rev 3233)
@@ -0,0 +1,387 @@
+#!/bin/ksh 
+
+# test suite for merge_obs_sequence utility
+
+# set up constant part at beginning
+cat > input.nml.head <<EOF
+&obs_sequence_nml
+   write_binary_obs_sequence = .false.  /
+
+&obs_kind_nml
+   assimilate_these_obs_types = 'RAW_STATE_VARIABLE'  /
+
+&utilities_nml
+   TERMLEVEL = 1,
+   module_details = .false.,
+   logfilename = 'dart_log.out'  /
+
+
+EOF
+
+# we will concatinate onto the end of this file
+rm -fr test_merge.log
+
+# should have a second arg - expects it to fail or not
+
+# set up functions which will be used for the rest of the script
+# shortone cats the entire result into the log, longone heads the
+# first 30 and last 30 lines
+function shortone
+{
+   rm -f input.nml
+   cat input.nml.head input.fragment > input.nml
+   echo "" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo " test $1 " >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo "" >> test_merge.log
+   cat input.fragment >> test_merge.log
+   echo "" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   rm -f obs_seq.merged
+   ./merge_obs_seq 2>&1 >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   if [[ -f obs_seq.merged ]]; then
+     cat obs_seq.merged >> test_merge.log
+   else
+     echo obs_seq.merged not found  >> test_merge.log
+   fi
+}
+
+function longone
+{
+   rm -f input.nml
+   cat input.nml.head input.fragment > input.nml
+   echo "" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo " test $1 " >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   echo "" >> test_merge.log
+   cat input.fragment >> test_merge.log
+   echo "" >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   rm -f obs_seq.merged
+   ./merge_obs_seq 2>&1 >> test_merge.log
+   echo "-------------------------" >> test_merge.log
+   if [[ -f obs_seq.merged ]]; then
+     head -30 obs_seq.merged >> test_merge.log
+     echo '-------------------------' >> test_merge.log
+     tail -30 obs_seq.merged >> test_merge.log
+     echo '-------------------------' >> test_merge.log
+   else
+     echo obs_seq.merged not found  >> test_merge.log
+   fi
+}
+
+###############################
+cat - > input.fragment <<EOF
+
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.A',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = -1,
+   first_obs_seconds        = -1,
+   last_obs_days            = -1,
+   last_obs_seconds         = -1,
+  /
+
+EOF
+shortone with_self works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.A',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone with_self_no_times works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 1,
+   filename_seq    = 'obs_seq.A',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = -1,
+   first_obs_seconds        = -1,
+   last_obs_days            = -1,
+   last_obs_seconds         = -1,
+  /
+EOF
+
+shortone self_only works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.B',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_fail fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.C',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_fail fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.D',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_fail fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.E',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_fail fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.F',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_fail fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 2,
+   filename_seq    = 'obs_seq.A', 'obs_seq.G',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+shortone should_work works
+
+
+###############################
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+  /
+EOF
+
+longone case_0 works
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 0,
+   last_obs_days            = 0,
+   last_obs_seconds         = 4000,
+  /
+EOF
+
+longone case_1 works
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 7000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 11000,
+  /
+EOF
+
+longone case_2 works
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 20000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 25000,
+  /
+EOF
+
+longone case_3 works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 15000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 16000,
+  /
+EOF
+
+longone case_4 fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 0,
+   last_obs_days            = 0,
+   last_obs_seconds         = 2000,
+  /
+EOF
+
+longone case_5 fails
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 3,
+   filename_seq    = 'obs_seq.L', 'obs_seq.M', 'obs_seq.N',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 25000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 28000,
+  /
+EOF
+
+longone case_6 fails
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 0,
+   last_obs_days            = 0,
+   last_obs_seconds         = 10000,
+  /
+EOF
+
+longone case_7 works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 13000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 25000,
+  /
+EOF
+
+longone case_8 works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 4000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 7000,
+  /
+EOF
+
+longone case_9 works
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 7200,
+   last_obs_days            = 0,
+   last_obs_seconds         = 9000,
+  /
+EOF
+
+longone case_9a works
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 10000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 11000,
+  /
+EOF
+
+longone case_9b works
+
+
+###############################
+cat > input.fragment <<EOF
+&merge_obs_seq_nml
+   num_input_files = 4,
+   filename_seq    = 'obs_seq.O', 'obs_seq.P', 'obs_seq.Q', 'obs_seq.R',
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = 0,
+   first_obs_seconds        = 10000,
+   last_obs_days            = 0,
+   last_obs_seconds         = 18000,
+  /
+EOF
+
+longone case_10 works
+
+

Modified: DART/trunk/obs_sequence/merge_obs_seq.f90
===================================================================
--- DART/trunk/obs_sequence/merge_obs_seq.f90	2008-02-13 16:49:34 UTC (rev 3232)
+++ DART/trunk/obs_sequence/merge_obs_seq.f90	2008-02-13 17:08:08 UTC (rev 3233)
@@ -15,14 +15,15 @@
 use    utilities_mod, only : timestamp, register_module, initialize_utilities, &
                              find_namelist_in_file, check_namelist_read, &
                              error_handler, E_ERR, E_MSG, logfileunit
-use time_manager_mod, only : time_type, operator(>), print_time
+use time_manager_mod, only : time_type, operator(>), print_time, set_time
 use obs_sequence_mod, only : obs_sequence_type, obs_type, write_obs_seq, &
                              init_obs, init_obs_sequence, static_init_obs_sequence, &
                              read_obs_seq_header, read_obs_seq, assignment(=), &
                              get_num_obs, get_first_obs, get_last_obs, get_next_obs, &
                              insert_obs_in_seq, get_num_copies, get_num_qc, &
                              get_copy_meta_data, get_qc_meta_data, set_qc_meta_data, &
-                             destroy_obs, destroy_obs_sequence
+                             destroy_obs, destroy_obs_sequence, delete_seq_head, &
+                             delete_seq_tail, get_num_key_range, set_copy_meta_data
 
 implicit none
 
@@ -32,18 +33,17 @@
    revision = "$Revision$", &
    revdate  = "$Date$"
 
-type(obs_sequence_type) :: seq1, seq2
+type(obs_sequence_type) :: seq_in, seq_out
 type(obs_type)          :: obs, prev_obs, next_obs, new_obs
 logical                 :: is_there_one, is_this_last
-integer                 :: size_seq1, num_copies1, num_qc1
-integer                 :: size_seq2, num_copies2, num_qc2
-integer                 :: size_seq,  num_copies,  num_qc
-integer                 :: add_size_seq = 0
-integer                 :: add_copies = 0, add_qc = 0
-integer                 :: num_inserted, iunit, io, i, total_num_inserted
-integer                 :: max_num_obs, file_id
-character(len = 129)    :: read_format
-logical                 :: pre_I_format
+integer                 :: size_seq_in, num_copies_in, num_qc_in
+integer                 :: size_seq_out, num_copies_out, num_qc_out
+integer                 :: num_inserted, iunit, io, i, j, total_num_inserted
+integer                 :: max_num_obs, file_id, remaining_obs_count
+integer                 :: first_seq
+character(len = 129)    :: read_format, meta_data
+logical                 :: pre_I_format, all_gone
+logical                 :: trim_first, trim_last
 character(len = 129)    :: msgstring
 
 !----------------------------------------------------------------
@@ -55,9 +55,20 @@
 
 character(len = 129) :: filename_seq(max_num_input_files)
 character(len = 129) :: filename_out  = 'obs_seq.merged'
+logical              :: process_file(max_num_input_files)
 
-namelist /merge_obs_seq_nml/ num_input_files, filename_seq, filename_out
+! Time of first and last observations to be used from obs_sequence
+! If negative, these are not used
+integer  :: first_obs_days    = -1
+integer  :: first_obs_seconds = -1
+integer  :: last_obs_days     = -1
+integer  :: last_obs_seconds  = -1
+type(time_type) :: first_obs_time, last_obs_time
 
+
+namelist /merge_obs_seq_nml/ num_input_files, filename_seq, filename_out, &
+         first_obs_days, first_obs_seconds, last_obs_days, last_obs_seconds
+
 !----------------------------------------------------------------
 ! Start of the routine.
 ! This routine basically opens the second observation sequence file
@@ -92,11 +103,39 @@
 
 ! Read header information for the sequences to see if we need
 ! to accomodate additional copies or qc values from subsequent sequences.
-! Also, calculate how many observation to be added to the first sequence.
-add_copies   = 0
-add_qc       = 0
-add_size_seq = 0
+! Also, calculate how many observations to be added to the first sequence.
+num_copies_out   = 0
+num_qc_out       = 0
+size_seq_out     = 0
 
+! check to see if we are going to trim the sequence by time
+if(first_obs_seconds >= 0 .or. first_obs_days >= 0) then
+   first_obs_time = set_time(first_obs_seconds, first_obs_days)
+   trim_first = .true.
+else
+   trim_first = .false.
+endif
+if(last_obs_seconds >= 0 .or. last_obs_days >= 0) then
+   last_obs_time = set_time(last_obs_seconds, last_obs_days)
+   trim_last = .true.
+else
+   trim_last = .false.
+endif
+if (trim_first .and. trim_last) then
+   if (first_obs_time > last_obs_time) then
+      call error_handler(E_ERR,'merge_obs_seq', 'first time cannot be later than last time', &
+                         source,revision,revdate)
+   endif
+endif
+
+! TWO PASS algorithm; open each file, trim it if requested, and count
+! the number of actual observations.  then the output file can be
+! created with the correct size, and as observations are put into it
+! they'll be sorted, and unused obs will be removed.
+
+! pass 1:
+
+first_seq = -1
 do i = 1, num_input_files
 
    if ( len(filename_seq(i)) .eq. 0 .or. filename_seq(i) .eq. "" ) then
@@ -104,102 +143,143 @@
          'num_input_files and filename_seq mismatch',source,revision,revdate)
    endif
 
-   if ( i .eq. 1) then
-      ! for the header of the first seq
-      call read_obs_seq_header(filename_seq(i), num_copies1, num_qc1, size_seq1, &
-         max_num_obs, file_id, read_format, pre_I_format, close_the_file = .true.)
+   ! count up the number of observations we are going to eventually have.
+   ! if all the observations in a file are not part of the linked list, the
+   ! output number of observations might be much smaller than the total size in 
+   ! the header.  it is slower, but go ahead and read in the entire sequence
+   ! and count up the real number of obs - trim_seq will do the count even if
+   ! it is not trimming in time.  this allows us to create an empty obs_seq
+   ! output file of exactly the right size.
+
+   call read_obs_seq_header(filename_seq(i), num_copies_in, num_qc_in, size_seq_in, &
+      max_num_obs, file_id, read_format, pre_I_format, close_the_file = .true.)
+   
+   call read_obs_seq(filename_seq(i), 0, 0, 0, seq_in)
+   call trim_seq(seq_in, trim_first, first_obs_time, trim_last, last_obs_time,   &
+                 filename_seq(i), .true., remaining_obs_count)
+   call destroy_obs_sequence(seq_in)
+   if (remaining_obs_count == 0) then
+      process_file(i) = .false.
+      cycle
    else
-      call read_obs_seq_header(filename_seq(i), num_copies2, num_qc2, size_seq2, &
-         max_num_obs, file_id, read_format, pre_I_format, close_the_file = .true.)
-      add_size_seq = add_size_seq + size_seq2
-      if (num_copies2 > num_copies1) then 
-         add_copies  = num_copies2 - num_copies1
-         num_copies1 = num_copies2
-      endif
-      if (num_qc2 > num_qc1) then
-         add_qc  = num_qc2 - num_qc1
-         num_qc1 = num_qc2
-      endif
+      process_file(i) = .true.
+      size_seq_in = remaining_obs_count
    endif
 
+   if ( first_seq < 0 ) then
+      first_seq = i
+      num_copies_out = num_copies_in
+      num_qc_out = num_qc_in
+      size_seq_out = size_seq_in
+   else
+      size_seq_out = size_seq_out + size_seq_in
+   endif
+
 enddo
 
-! Read 1st obs seq, expand its size for insertion
-call read_obs_seq(filename_seq(1), add_copies, add_qc, add_size_seq, seq1)
-size_seq    = get_num_obs(seq1)      ! does not include size_seq2
-num_copies  = get_num_copies(seq1)   ! already includes add_copies
-num_qc      = get_num_qc(seq1)       ! already includes add_qc
+! no valid obs found?  if the index value is still negative, we are
+! still waiting to process the first one and never found one.
+if (first_seq < 0 .or. size_seq_out == 0) then
+   msgstring = 'All input files are empty or all obs outside the first/last times'
+   call error_handler(E_ERR,'merge_obs_seq',msgstring,source,revision,revdate)
+endif
 
+! pass 2:
+
 ! Initialize individual observation variables 
-call init_obs(     obs, num_copies, num_qc)
-call init_obs( new_obs, num_copies, num_qc)
-call init_obs(next_obs, num_copies, num_qc)
-call init_obs(prev_obs, num_copies, num_qc)
+call init_obs(     obs, num_copies_out, num_qc_out)
+call init_obs( new_obs, num_copies_out, num_qc_out)
+call init_obs(next_obs, num_copies_out, num_qc_out)
+call init_obs(prev_obs, num_copies_out, num_qc_out)
 
 total_num_inserted = 0
 
-! Read obs seq to be added, and insert obs from it to the first seq
-do i = 2, num_input_files
+! Read obs seq to be added, and insert obs from it to the output seq
+first_seq = -1
+do i = 1, num_input_files
 
-   call read_obs_seq(filename_seq(i), 0, 0, 0, seq2)
+   if (.not. process_file(i)) cycle
+ 
+   write(msgstring,*) 'Starting to process input sequence file ', trim(filename_seq(i))
+   call error_handler(E_MSG,'merge_obs_seq',msgstring,source,revision,revdate)
 
-   size_seq1 = get_num_obs(seq1)     !current size of seq1
-   size_seq2 = get_num_obs(seq2)     !current size of seq2
+   call read_obs_seq(filename_seq(i), 0, 0, 0, seq_in)
 
-   ! Compare metadata between the observation sequences.
-   ! If it is compatible, keep going, if not ... it will terminate here.
-   call compare_metadata(seq1, seq2)
+   ! If you get here, there better be observations in this file which
+   ! are going to be used (the process_file flag wouldn't be set otherwise.)
+   call trim_seq(seq_in, trim_first, first_obs_time, trim_last, last_obs_time,   &
+                 filename_seq(i), .false., remaining_obs_count)
 
-   call error_handler(E_MSG,'merge_obs_seq', &
-       'Good news - observation sequence files compatible ...', source,revision,revdate)
+   ! This would be an error at this point.
+   if(remaining_obs_count == 0) then
+      call destroy_obs_sequence(seq_in) 
+      write(msgstring, *) 'Internal error trying to process file ', trim(filename_seq(i))
+      call error_handler(E_ERR,'merge_obs_seq',msgstring,source,revision,revdate)
+   endif
 
-   ! Getting the time of the last observation in the first sequence to see
-   ! if we can append instead of insert. Appending is MUCH faster.
-   is_there_one = get_last_obs(seq1, obs)
-   if (.not. is_there_one .and. size_seq1 >= 1) then
-      call error_handler(E_ERR,'merge_obs_seq', &
-       'BAD news - first obs_seq is neverending ...', source,revision,revdate) 
+   ! create the output sequence here based on the first input file
+   if (first_seq < 0) then
+      call init_obs_sequence(seq_out, num_copies_out, num_qc_out, size_seq_out) 
+      do j=1, num_copies_out
+	 meta_data = get_copy_meta_data(seq_in, j) 
+         call set_copy_meta_data(seq_out, j, meta_data)
+      enddo 
+      do j=1, num_qc_out
+	 meta_data = get_qc_meta_data(seq_in, j) 
+         call set_qc_meta_data(seq_out, j, meta_data)
+      enddo 
+      first_seq = i
+   else
+      ! we have an existing output sequence already.  make sure the next one
+      ! is completely compatible.
+
+      ! Compare metadata between the observation sequences.
+      ! This routine exits if they do not match.
+      call compare_metadata(seq_out, seq_in, filename_seq(first_seq), filename_seq(i))
    endif
 
+   size_seq_out = get_num_key_range(seq_out)   !current size of seq_out
+   size_seq_in = get_num_key_range(seq_in)     !current size of seq_in
+
    !-------------------------------------------------------------
-   ! Start to insert obs from sequence 2 into sequence 1
+   ! Start to insert obs from sequence_in into sequence_out
    !
    ! NOTE: insert_obs_in_seq CHANGES the obs passed in.
    !       Must pass a copy of incoming obs to insert_obs_in_seq.
    !--------------------------------------------------------------
    num_inserted = 0
-   is_there_one = get_first_obs(seq2, obs)
+   is_there_one = get_first_obs(seq_in, obs)
 
    if ( is_there_one )  then
 
-      new_obs      = obs           ! obs records position in seq2
+      new_obs      = obs           ! obs records position in seq_out
 
-      call insert_obs_in_seq(seq1, new_obs)  ! new_obs linked list info changes
+      call insert_obs_in_seq(seq_out, new_obs)  ! new_obs linked list info changes
 
-      prev_obs     = new_obs       ! records new position in seq1
+      prev_obs     = new_obs       ! records new position in seq_in
       num_inserted = num_inserted + 1
    
-      call get_next_obs(seq2, obs, next_obs, is_this_last)
+      call get_next_obs(seq_in, obs, next_obs, is_this_last)
       ObsLoop : do while ( .not. is_this_last)
 
          if (mod(num_inserted,1000) == 0) then
-            print*, 'inserted number ',num_inserted,' of ',size_seq2
+            print*, 'inserted number ',num_inserted,' of ',size_seq_in
          endif
 
-         obs     = next_obs   ! essentially records position in seq2
-         new_obs = obs        ! will be modified w/ position in seq1
+         obs     = next_obs   ! essentially records position in seq_out
+         new_obs = obs        ! will be modified w/ position in seq_in
 
          ! Since the stride through the observation sequence file is always 
          ! guaranteed to be in temporally-ascending order, we can use the
          ! 'previous' observation as the starting point to search for the
-         ! correct insertion point. 
+         ! correct insertion point.  This speeds up the insert code a lot.
 
-         call insert_obs_in_seq(seq1, new_obs, prev_obs)
+         call insert_obs_in_seq(seq_out, new_obs, prev_obs)
 
-         prev_obs     = new_obs    ! update position in seq1 for next insert
+         prev_obs     = new_obs    ! update position in seq_in for next insert
          num_inserted = num_inserted + 1
 
-         call get_next_obs(seq2, obs, next_obs, is_this_last)
+         call get_next_obs(seq_in, obs, next_obs, is_this_last)
 
       enddo ObsLoop
 
@@ -211,25 +291,23 @@
    endif
 
    print*, '--------------  Obs seq file # :          ', i
-   print*, 'Number of obs in previous seq  :          ', size_seq1
-   print*, 'Number of obs to be  inserted  :          ', size_seq2
+   print*, 'Number of obs in previous seq  :          ', size_seq_out
+   print*, 'Number of obs to be  inserted  :          ', size_seq_in
    print*, 'Number of obs really inserted  :          ', num_inserted
    print*, '---------------------------------------------------------'
 
-   call destroy_obs_sequence(seq2)
+   call destroy_obs_sequence(seq_in)
 
 enddo
 
-print*, 'Number of obs in first seq     :          ', size_seq
 print*, 'Total number of obs  inserted  :          ', total_num_inserted
-print*, 'Target number of obs in the new seq file :', size_seq + total_num_inserted
-print*, 'Actual number of obs in the new seq file :', get_num_obs(seq1)
+print*, 'Actual number of obs in the new seq file :', get_num_key_range(seq_out)
 
-call write_obs_seq(seq1, filename_out)
+call write_obs_seq(seq_out, filename_out)
 
 ! Time to clean up
 
-call destroy_obs_sequence(seq1)
+call destroy_obs_sequence(seq_out)
 call destroy_obs(     obs)
 call destroy_obs( new_obs)
 call destroy_obs(next_obs)
@@ -253,8 +331,7 @@
 end subroutine merge_obs_seq_modules_used
 
 
-  subroutine compare_metadata(seq1, seq2)
-! subroutine compare_metadata(seq1, seq2)
+  subroutine compare_metadata(seq1, seq2, fname1, fname2)
 !
 ! This subroutine compares the metadata for two different observation
 ! sequences and terminates the program if they are not conformable.
@@ -265,39 +342,45 @@
 !
 
  type(obs_sequence_type), intent(IN) :: seq1, seq2
+ character(len=*), optional :: fname1, fname2
 
 integer :: num_copies1, num_qc1
 integer :: num_copies2, num_qc2
 integer :: num_copies , num_qc, i
 character(len=129) :: str1, str2
-character(len=255) :: msgstring
+character(len=255) :: msgstring1, msgstring2
 
 num_qc1     = get_num_qc(    seq1)
-size_seq1   = get_num_obs(   seq1)
 num_copies1 = get_num_copies(seq1)
 
 num_qc2     = get_num_qc(    seq2)
-size_seq2   = get_num_obs(   seq2)
 num_copies2 = get_num_copies(seq2)
 
 num_copies  = num_copies1
 num_qc      = num_qc1
 
+! get this ready in case we have to use it
+if (present(fname1) .and. present(fname2)) then
+   write(msgstring1,*)'Sequence files ', trim(fname1), ' and ', trim(fname2), &
+                      ' are not compatible'
+else
+  msgstring1 = 'Sequence files cannot be merged because they are not compatible'
+endif
+
 if ( num_copies1 /= num_copies2 ) then
-   write(msgstring,*)'The obs_sequences have incompatible numbers of copies', &
-                      num_copies1, num_copies2 
-   call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
+   write(msgstring2,*)'Different numbers of data copies found: ', &
+                      num_copies1, ' vs ', num_copies2 
+   call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
    num_copies = -1
 endif
 if ( num_qc1 /= num_qc2 ) then
-   write(msgstring,*)'The obs_sequences have incompatible numbers of QC metadata', &
-                      num_qc1, num_qc2
-   call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
+   write(msgstring2,*)'Different different numbers of QCs found: ', &
+                      num_qc1, ' vs ', num_qc2
+   call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
    num_qc = -1
 endif
 if ( num_copies < 0 .or. num_qc < 0 ) then
-   call error_handler(E_ERR, 'merge_obs_seq', &
-        'obs_sequence files incompatible ... stopping.', source, revision, revdate)
+   call error_handler(E_ERR, 'merge_obs_seq', msgstring1, source, revision, revdate)
 endif
 
 MetaDataLoop : do i=1, num_copies
@@ -305,15 +388,14 @@
    str2 = trim(adjustl(get_copy_meta_data(seq2,i)))
 
    if( str1 == str2 ) then
-      write(msgstring,*)'metadata ',trim(adjustl(str1)), ' in both.'
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
+      write(msgstring2,*)'metadata ',trim(adjustl(str1)), ' in both.'
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
    else
-      write(msgstring,*)'metadata seq1 ', trim(adjustl(str1))
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
-      write(msgstring,*)'metadata seq2 ', trim(adjustl(str2))
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
-      call error_handler(E_ERR, 'merge_obs_seq', &
-        'obs_sequence files incompatible ... stopping.', source, revision, revdate)
+      write(msgstring2,*)'metadata value mismatch. seq1: ', trim(adjustl(str1))
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
+      write(msgstring2,*)'metadata value mismatch. seq2: ', trim(adjustl(str2))
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
+      call error_handler(E_ERR, 'merge_obs_seq', msgstring1, source, revision, revdate)
    endif
 enddo MetaDataLoop
 
@@ -322,19 +404,61 @@
    str2 = trim(adjustl(get_qc_meta_data(seq2,i)))
 
    if( str1 == str2 ) then
-      write(msgstring,*)'qc metadata ', trim(adjustl(str1)), ' in both.'
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
+      write(msgstring2,*)'qc metadata ', trim(adjustl(str1)), ' in both.'
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
    else
-      write(msgstring,*)'qc metadata seq1 ', trim(adjustl(str1))
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
-      write(msgstring,*)'qc metadata seq2 ', trim(adjustl(str2))
-      call error_handler(E_MSG, 'merge_obs_seq', msgstring, source, revision, revdate)
-      call error_handler(E_ERR, 'merge_obs_seq', &
-        'obs_sequence files incompatible ... stopping.', source, revision, revdate)
+      write(msgstring2,*)'qc metadata value mismatch. seq1: ', trim(adjustl(str1))
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
+      write(msgstring2,*)'qc metadata value mismatch. seq2: ', trim(adjustl(str2))
+      call error_handler(E_MSG, 'merge_obs_seq', msgstring2, source, revision, revdate)
+      call error_handler(E_ERR, 'merge_obs_seq', msgstring1, source, revision, revdate)
    endif
 enddo QCMetaData
 
 end subroutine compare_metadata
 
+! pass in an already opened sequence and a start/end time.  this routine
+! really trims the observations out of the sequence, and returns a count
+! of how many remain.
+subroutine trim_seq(seq, trim_first, first_time, trim_last, last_time, seqfilename, &
+                    print_msg, remaining_obs_count)
+ type(obs_sequence_type), intent(inout) :: seq
+ logical, intent(in)                    :: trim_first, trim_last
+ type(time_type), intent(in)            :: first_time, last_time
+ character(len = *), intent(in)         :: seqfilename
+ logical, intent(in)                    :: print_msg
+ integer, intent(out)                   :: remaining_obs_count
 
+   ! Need to find first obs with appropriate time, delete all earlier ones
+   if(trim_first) then
+      call delete_seq_head(first_time, seq, all_gone)
+      if(all_gone) then
+         if (print_msg) then
+            msgstring = 'Skipping: all obs in ' // trim(seqfilename) // &
+                        ' are before first_obs_days:first_obs_seconds'
+            call error_handler(E_MSG,'merge_obs_seq',msgstring,source,revision,revdate)
+         endif
+         remaining_obs_count = 0
+         return
+      endif
+   endif
+   
+   ! Also get rid of observations past the last_obs_time if requested
+   if(trim_last) then
+      call delete_seq_tail(last_time, seq, all_gone)
+      if(all_gone) then
+         if (print_msg) then
+            msgstring = 'Skipping: all obs in ' // trim(seqfilename) // &
+                        ' are after last_obs_days:last_obs_seconds'
+            call error_handler(E_MSG,'merge_obs_seq',msgstring,source,revision,revdate)
+         endif
+         remaining_obs_count = 0
+         return
+      endif
+   endif
+   
+   remaining_obs_count = get_num_key_range(seq)
+
+end subroutine trim_seq
+
 end program merge_obs_seq

Modified: DART/trunk/obs_sequence/merge_obs_seq.html
===================================================================
--- DART/trunk/obs_sequence/merge_obs_seq.html	2008-02-13 16:49:34 UTC (rev 3232)
+++ DART/trunk/obs_sequence/merge_obs_seq.html	2008-02-13 17:08:08 UTC (rev 3233)
@@ -59,16 +59,35 @@
 <H2>OVERVIEW</H2>
 
 <P>
-This program can merge two or more compatible observation sequences 
-and create a single observation sequence file with the 
-combined observations. The number of input files, their filenames,
-and the output filename are read from the namelist file.
+This program merges one or more compatible observation sequences 
+into a single observation sequence file.
+The number of input files, their filenames,
+and the output filename are read from the
+<em class=code>&#38;merge_obs_seq_nml</em> namelist 
+in file <em class=file>input.nml</em>.
 <BR><BR>
-This program is also a convenient way to convert observation sequence
-files from ASCII to (more compact) binary, or vice-versa. Simply specify
-that there is 1 input file. The output format is specified by the 
+The observations copied to the output file can be restricted in
+time by setting the namelist items for first and last observation
+timestamps (in Gregorian days and seconds).
+All observations before the start time and 
+after the last time will be removed before merging. 
+It is ok for some of the input
+files to have no observations in the requested time range, and 
+the files can have overlapping time ranges.
+<BR><BR>
+<em class=unix>merge_obs_seq</em> does several things which can
+be useful even when there is only a single input file.
+The program will always sort the output observation
+sequence in increasing time order, and will not copy
+any unreferenced observations from the input sequence. 
+It can also be used to convert an observation sequence file from
+ASCII to (more compact) binary, or vice-versa. 
+The output format is specified by the 
 <em class=code>&#38;obs_sequence_nml</em> namelist 
 in file <em class=file>input.nml</em>.
+To process a single input file,
+set the number of input files to 1, and merge from an existing filename
+into a new file.
 <BR><BR>
 This routine also uses a MUCH faster insertion method than the
 versions that used only two input files. A test on
@@ -78,13 +97,6 @@
 where you inserted the last one greatly simplifies the logic of where
 one starts looking to insert the next observation. Consequently, inserting
 and appending are now equally fast. Snappy!
-<BR><BR>
-<em class=unix>merge_obs_seq</em> can be used to sort observations in an
-observation sequence as well as physically delete broken nodes from 
-the sequence. The only trick is to merge with an empty 
-<em class=file>obs_seq</em> file. The empty <em class=file>obs_seq</em> 
-must be specified first in the list of files to merge, it has to have a header, 
-and first = last = -1. Pretty Sneaky.
 </P>
 
 
@@ -108,7 +120,8 @@
  '&#38;' and terminating with a slash '/'.
  </P>
  <div class=namelist><pre>
- <em class=call>namelist / merge_obs_seq / </em> num_input_files, filename_seq, filename_out
+ <em class=call>namelist / merge_obs_seq_nml / </em> num_input_files, filename_seq,
+  filename_out, first_obs_days, first_obs_seconds, last_obs_days, last_obs_seconds
  </pre></div>
 
  <H3 class=indent1>Discussion</H3>
@@ -143,6 +156,28 @@
      <!--  type  --><TD>character(len=129)</TD>
      <!--descript--><TD>The name of the resulting (merged) observation sequence file.
                         Default: 'obs_seq.merged'</TD></TR>
+ <TR><!--contents--><TD valign=top>first_obs_days</TD>
+     <!--  type  --><TD>integer</TD>
+     <!--descript--><TD>If non-negative, restrict the timestamps of the observations
+                        copied to the merged file to be equal to or after this date
+                        (specified in the Gregorian calendar; day number since 1600).
+                        Default: -1, merge all observations</TD></TR>
+ <TR><!--contents--><TD valign=top>first_obs_seconds</TD>
+     <!--  type  --><TD>integer</TD>
+     <!--descript--><TD>If non-negative, restrict the timestamps of the observations
+                        copied to the merged file to be equal to or after this time.
+                        Default: -1, merge all observations</TD></TR>
+ <TR><!--contents--><TD valign=top>last_obs_days</TD>
+     <!--  type  --><TD>integer</TD>
+     <!--descript--><TD>If non-negative, restrict the timestamps of the observations
+                        copied to the merged file to be equal to or before this date
+                        (specified in the Gregorian calendar; day number since 1600).
+                        Default: -1, merge all observations</TD></TR>
+ <TR><!--contents--><TD valign=top>last_obs_seconds</TD>
+     <!--  type  --><TD>integer</TD>
+     <!--descript--><TD>If non-negative, restrict the timestamps of the observations
+                        copied to the merged file to be equal to or before this time.
+                        Default: -1, merge all observations</TD></TR>
  </TABLE>
  
 

Modified: DART/trunk/obs_sequence/merge_obs_seq.nml
===================================================================
--- DART/trunk/obs_sequence/merge_obs_seq.nml	2008-02-13 16:49:34 UTC (rev 3232)
+++ DART/trunk/obs_sequence/merge_obs_seq.nml	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,5 +1,9 @@
 &merge_obs_seq_nml
    num_input_files = 2,
    filename_seq    = 'obs_seq.one', 'obs_seq.two',
-   filename_out    = 'obs_seq.merged'  /
+   filename_out    = 'obs_seq.merged',
+   first_obs_days           = -1,
+   first_obs_seconds        = -1,
+   last_obs_days            = -1,
+   last_obs_seconds         = -1  /
 

Modified: DART/trunk/obs_sequence/obs_sequence_mod.f90
===================================================================
--- DART/trunk/obs_sequence/obs_sequence_mod.f90	2008-02-13 16:49:34 UTC (rev 3232)
+++ DART/trunk/obs_sequence/obs_sequence_mod.f90	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1,6 +1,6 @@
-! Data Assimilation Research Testbed -- DART
-! Copyright 2004-2007, Data Assimilation Research Section
-! University Corporation for Atmospheric Research
+! Data Assimilation Research Testbed -- DART 
+! Copyright 2004-2008, Data Assimilation Research Section 
+! University Corporation for Atmospheric Research 
 ! Licensed under the GPL -- www.gpl.org/licenses/gpl.html
 
 module obs_sequence_mod
@@ -32,9 +32,9 @@
 use time_manager_mod, only : time_type, operator(>), operator(<), operator(>=), &
                              operator(/=), set_time, operator(-), operator(+), &
                              operator(==)
-use    utilities_mod, only : get_unit, close_file, find_namelist_in_file, check_namelist_read, &
-                             register_module, error_handler, E_ERR, E_WARN, E_MSG, logfileunit, &
-                             do_output
+use    utilities_mod, only : get_unit, close_file, register_module, error_handler, &
+                             find_namelist_in_file, check_namelist_read, &
+                             E_ERR, E_WARN, E_MSG, logfileunit, do_output
 use     obs_kind_mod, only : write_obs_kind, read_obs_kind
 
 
@@ -50,10 +50,12 @@
    get_num_copies, get_num_qc, get_num_obs, get_max_num_obs, get_copy_meta_data, &
    get_qc_meta_data, get_next_obs, get_prev_obs, insert_obs_in_seq, &
    delete_obs_from_seq, set_copy_meta_data, set_qc_meta_data, get_first_obs, &
-   get_last_obs, add_copies, add_qc, write_obs_seq, read_obs_seq, &
-   append_obs_to_seq, get_obs_from_key, get_obs_time_range, set_obs, get_time_range_keys, &
-   get_num_times, static_init_obs_sequence, destroy_obs_sequence, read_obs_seq_header, &
-   get_expected_obs, delete_seq_head, delete_seq_tail, get_next_obs_from_key, get_prev_obs_from_key
+   get_last_obs, add_copies, add_qc, write_obs_seq, read_obs_seq, set_obs, &
+   append_obs_to_seq, get_obs_from_key, get_obs_time_range, get_time_range_keys, &
+   get_num_times, get_num_key_range, &
+   static_init_obs_sequence, destroy_obs_sequence, read_obs_seq_header, &
+   get_expected_obs, delete_seq_head, delete_seq_tail, &
+   get_next_obs_from_key, get_prev_obs_from_key
 
 ! Public interfaces for obs
 public :: obs_type, init_obs, destroy_obs, get_obs_def, set_obs_def, &
@@ -75,11 +77,15 @@
    integer :: num_qc
    integer :: num_obs
    integer :: max_num_obs
-   character(len = 129), pointer :: copy_meta_data(:)
+! F95 allows pointers to be initialized to a known value
+   !character(len = 129), pointer :: copy_meta_data(:)  => NULL()
+   !character(len = 129), pointer :: qc_meta_data(:)    => NULL()
+   character(len = 129), pointer :: copy_meta_data(:) 
    character(len = 129), pointer :: qc_meta_data(:)
    integer :: first_time
    integer :: last_time
 !   integer :: first_avail_time, last_avail_time
+   !type(obs_type), pointer :: obs(:)   => NULL()
    type(obs_type), pointer :: obs(:) 
 ! What to do about groups
 end type obs_sequence_type
@@ -90,6 +96,8 @@
 ! Do I want to enforce the identity of the particular obs_sequence?
    integer :: key
    type(obs_def_type) :: def
+   !real(r8), pointer :: values(:)  => NULL()
+   !real(r8), pointer :: qc(:)      => NULL()
    real(r8), pointer :: values(:) 
    real(r8), pointer :: qc(:)
 ! Put sort indices directly into the data structure
@@ -146,7 +154,7 @@
 !--------------------------------------------------------------
 
 !WHAT ABOUT PASS THROUGHS TO THE OBS_DEF???
-! WhAT ABOUT copy_obs_sequence similar to read.
+! WHAT ABOUT copy_obs_sequence similar to read.
 !-------------------------------------------------
 subroutine init_obs_sequence(seq, num_copies, num_qc, &
    expected_max_num_obs)
@@ -205,16 +213,28 @@
 
 if ( seq%max_num_obs > 0 ) then
 
-   if (associated(seq%copy_meta_data)) deallocate(seq%copy_meta_data)
-   if (associated(seq%qc_meta_data))   deallocate(seq%qc_meta_data)
+   if (associated(seq%copy_meta_data)) then
+      deallocate(seq%copy_meta_data)
+      nullify(seq%copy_meta_data)
+   endif
+   if (associated(seq%qc_meta_data)) then
+      deallocate(seq%qc_meta_data)
+      nullify(seq%qc_meta_data)
+   endif
           
    do i = 1, seq%max_num_obs
+   ! seq%obs is a derived type, not a pointer.
    !    if (associated(seq%obs(i))) call destroy_obs( seq%obs(i) )
-                                  call destroy_obs( seq%obs(i) )
+      call destroy_obs( seq%obs(i) )
    end do
 
    ! Also free up the obs storage in the sequence
-   if(associated(seq%obs)) deallocate(seq%obs)
+   if(associated(seq%obs)) then 
+      deallocate(seq%obs)
+      nullify(seq%obs)
+   else
+      print *, 'destroy_obs_sequence called but seq%obs not associated'
+   endif
 
    seq%first_time  = -1
    seq%last_time   = -1
@@ -1364,7 +1384,7 @@
       ! Whole sequence is after
       all_gone = .false.
    else
-      ! Whole sequence is before
+      ! Whole sequence is before; but sequence is not altered?
       all_gone = .true.
    endif
    ! Destroy temp storage and return
@@ -1372,6 +1392,15 @@
    return
 endif
 
+! compare num_keys with all possible keys in file; if equal, you have
+! also removed all obs and should return all_gone = .true.  
+if (num_keys == get_num_key_range(seq)) then
+   all_gone = .true.
+   ! Destroy temp storage and return
+   call destroy_obs(obs)
+   return
+endif
+
 ! If here, then there are a set of observations that are not being used at beginning
 ! Delete them from the sequence
 all_gone = .false.
@@ -1443,6 +1472,15 @@
    return
 endif
 
+! compare num_keys with all possible keys in file; if equal, you have
+! also removed all obs and should return all_gone = .true.  
+if (num_keys == get_num_key_range(seq)) then
+   all_gone = .true.
+   ! Destroy temp storage and return
+   call destroy_obs(obs)
+   return
+endif
+
 ! If here, then there are a set of observations that are not being used at the end
 ! Delete them from the sequence
 all_gone = .false.
@@ -1462,7 +1500,6 @@
 end subroutine delete_seq_tail
 
 
-
 !=================================================
 
 ! Functions for the obs_type
@@ -1490,19 +1527,17 @@
 
 ! To be overloaded with =
 
-type(obs_type), intent(out) :: obs1
+!type(obs_type), intent(out) :: obs1
+type(obs_type), intent(inout) :: obs1
 type(obs_type), intent(in) :: obs2
 
 obs1%key = obs2%key
 call copy_obs_def(obs1%def, obs2%def)
 
-!write(*, *) 'in copy obs'
-!write(*, *) 'size of obs1, obs2 ', size(obs1%values), size(obs2%values)
 if (.not.associated(obs1%values) .or. .not.associated(obs1%qc) .or. &
     size(obs1%values) /= size(obs2%values) .or. size(obs1%qc) /= size(obs2%qc)) then
    if (associated(obs1%values)) deallocate(obs1%values)
    if (associated(obs1%qc)) deallocate(obs1%qc)
-   !write(*, *) 'allocating in copy_obs'
    allocate(obs1%values(size(obs2%values)), obs1%qc(size(obs2%qc)))
 endif
 obs1%values = obs2%values
@@ -1511,8 +1546,6 @@
 obs1%next_time = obs2%next_time
 obs1%cov_group = obs2%cov_group
 
-!write(*, *) 'done with copy_obs'
-
 end subroutine copy_obs
 
 !-------------------------------------------------
@@ -1522,7 +1555,16 @@
 ! Free up allocated storage in an observation type
 type(obs_type), intent(inout) :: obs
 
-deallocate(obs%values, obs%qc)
+if (associated(obs%values)) then
+   deallocate(obs%values)
+   nullify(obs%values)
+endif
+if (associated(obs%qc)) then
+   deallocate(obs%qc)
+   nullify(obs%qc)
+endif
+!if pointers are nullified() then this is safe (and simpler).
+!deallocate(obs%values, obs%qc)
 call destroy_obs_def(obs%def)
 
 end subroutine destroy_obs
@@ -1541,7 +1583,7 @@
 !-------------------------------------------------
 subroutine set_obs_def(obs, obs_def)
 
-type(obs_type), intent(out) :: obs
+type(obs_type), intent(inout) :: obs
 type(obs_def_type), intent(in) :: obs_def
 
 call copy_obs_def(obs%def, obs_def)
@@ -1855,7 +1897,53 @@
 
 end function get_num_times
 
+!---------------------------------------------------------
 
+function get_num_key_range(seq, key1, key2)
+
+! Returns number of observations between the two given keys
+
+type(obs_sequence_type), intent(in) :: seq
+integer, optional, intent(in) :: key1, key2
+integer :: get_num_key_range
+
+integer :: next, last
+
+
+if (present(key1)) then
+   if (key1 < seq%first_time .or. key1 > seq%last_time) then
+      write(msg_string, *) 'Bad value for key1, must be between ', &
+                            seq%first_time, ' and ', seq%last_time
+      call error_handler(E_ERR, 'get_num_key_range', msg_string, &
+         source, revision, revdate)
+   endif
+   next = key1
+else
+   next = seq%first_time
+endif
+if (present(key2)) then
+   if (key2 < seq%first_time .or. key2 > seq%last_time) then
+      write(msg_string, *) 'Bad value for key2, must be between ', &
+                            seq%first_time, ' and ', seq%last_time
+      call error_handler(E_ERR, 'get_num_key_range', msg_string, &
+         source, revision, revdate)
+   endif
+   last = key2
+else
+   last = seq%last_time
+endif
+
+! count them up
+get_num_key_range = 0
+do while (next /= -1)
+   get_num_key_range = get_num_key_range + 1
+   if (next == last) exit
+   next = seq%obs(next)%next_time
+end do
+
+end function get_num_key_range
+
+
 !-------------------------------------------------
 !subroutine get_cov_group
 !-------------------------------------------------

Modified: DART/trunk/obs_sequence/obs_sequence_mod.html
===================================================================
--- DART/trunk/obs_sequence/obs_sequence_mod.html	2008-02-13 16:49:34 UTC (rev 3232)
+++ DART/trunk/obs_sequence/obs_sequence_mod.html	2008-02-13 17:08:08 UTC (rev 3233)
@@ -1075,6 +1075,38 @@
  </TABLE>
  <BR>
 
+<!--============= DESCRIPTION OF A FUNCTION ========================-->
+ <A NAME="get_num_key_range"></A>
+ <P></P><HR><P></P>
+ <div class=routine>
+ <em class=call> var = get_num_key_range(seq, key1, key2) </em>
+ <pre>
+ integer                             :: <em class=code>get_num_key_range</em>
+ type(obs_sequence_type), intent(in) :: <em class=code>seq</em>
+ integer, optional,       intent(in) :: <em class=code>key1, key2</em>
+ </pre></div>
+ <H3 class=indent1>Description</H3>
+ <P>
+Returns the number of observations between the two given keys.
+The default key numbers are the first and last in the sequence file.
+This routine can be used to count the actual number of observations
+in a sequence and will be accurate even if the sequence has been
+trimmed with delete_seq_head() or delete_seq_tail().
+ </P>
+ <TABLE width=100% border=0 summary="" celpadding=3>
+ <TR><TD valign=top><em class=code>var&nbsp; &nbsp; </em></TD>
+     <TD>Number of unique times for observations in a sequence</TD></TR>
+ <TR><TD valign=top><em class=code>seq&nbsp; &nbsp; </em></TD>
+     <TD>An observation sequence</TD></TR>
+ <TR><TD valign=top><em class=code>key1&nbsp; &nbsp; </em></TD>
+     <TD>The starting key number.  Defaults to the first observation
+         in the sequence.</TD></TR>
+ <TR><TD valign=top><em class=code>key2&nbsp; &nbsp; </em></TD>
+     <TD>The ending key number.  Defaults to the last observation
+         in the sequence.</TD></TR>
+ </TABLE>
+ <BR>
+
 <!--============= DESCRIPTION OF A SUBROUTINE =======================-->
  <A NAME="static_init_obs_sequence"></A>
  <P></P><HR><P></P>


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