Some of the major changes I did in this version are

(i) Configure the model using a namelist file
           The executable (qcom_3d.exe) will take an argument namelist=file.txt. A sample name list at the above URL has all the configurable options/parameters available in this version. 

(ii) Configure the model using command-line arguments:
          Sometimes we need to run the model parallelly with the almost same configuration except for changes in few parameters. For example, If I want to run the model with different sidewall temperatures, all the other configuration remains the same.  One option is to create multiple namelist with different sidewall temperatures and run them with the model. However, this option is tedious. Therefore, I allow for command-line model configuration.
          The command-line arguments should be one of the name-value pairs as in the name list, but with no spaces (e.g. theta_swall=285). The number of configurable name-value pairs at the command line is limited to 10. Please see the shell script "run_qcom_3d_batch2.sh" to see how it works. The command-line values will override the configuration in the name list file.

(iii) Sidewall as moisture sink:
   The implemented the sidewall BC to act as a sink under subroutine bound_w_swall. It seems to work and reduces the domain average water vapor and supersaturation.  I use the namelist parameter "qw_swall = -1" to configure the sidewall as a sink. If this parameter is set to zero ("qw_swall = 0") then sidewalls have no moisture flux;

(iv)Model output:
          Model output is stored under the default folder ./data/test; If the experiment name is configured, then the output is stored in a folder with the same name. (e.g. exp_name = "swall_theta_285" will  have output under data/swall_theta_285);  The 3D domain average, standard deviation, maximum for all the variables are saved into respective files (iter_stats_avg.txt, iter_stats_std,iter_stats_max.txt). Also, the histogram for theta, qv, super-saturation are saved into different files (theta_hist.txt, qv_hist.txt,super_sat_hist.txt). I am generating histograms with 100 bins, but the number of bins can be changed in the namelist file.

Compiling the program
Since the code has grown to a thousand plus lines, I broke it into two files - "main.f90" and "common_variables.f90". The shell script "./compile_qcom_3d.sh" will compile the Fortran code to produce an executable qcom_3d.exe.

Running the model: There are two ways to run the model
1) Configure all the parameters in the namelist file and run as below
          qcom_3d.exe namelist=namelist.txt
2) Use default configurations in the namelist file and override them through few command-line options.
            qcom_3d.exe namelist=namelist.txt  exp_name=swall_theta_290  theta_wall=290