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This PR removes all calls to write(6,*) in the code that can be encountered during the course of a normal simulation. Instead, stdout%print is used, which is redirected to a log file, if desired. This change prevents a situation where some error message could be written out to standard out, whereas others would appear in the log file. Note that several references to write(6,*) have been retained. These are not encountered during normal usage of the code and can still be helpful for debugging. In addition, many references to write(6,*) which were commented out or unnecessary have been removed. This PR fixes issue #325 .