Add the logo and the reference to the tacoxDNA paper to the README

README.md

@@ -1,6 +1,10 @@
-# tacoxDNA
+# tacox<img src="logo.png" width="35">NA
 
-tacoxDNA (Tools and Converters for oxDNA) is a collection of tools initially developed to help [oxDNA](http://dna.physics.ox.ac.uk/) users. However, it will soon be expanded so as to support additional models. The sections that follow introduce the tools and their usage.
+tacoxDNA (Tools and Converters for oxDNA) is a collection of tools initially developed to help [oxDNA](http://dna.physics.ox.ac.uk/) users. However, it will soon be expanded so as to support additional models. If you use tacoxDNA, please consider citing the following article:
+
+A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A. A. Louis, J. P. K. Doye, C. Micheletti and L. Rovigatti, ["TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami"](https://doi.org/10.1002/jcc.26029), *J. Comput. Chem.* (2019)
+
+The sections that follow introduce the tools and their usage.
 
 * [Generator for twisted and knotted configurations](#generator-for-twisted-and-knotted-configurations)
 * [oxDNA-to-LAMMPS converter](#oxdna-to-lammps-converter)
@@ -168,9 +172,9 @@ The `Tiamat_oxDNA.py` script converts [Tiamat](http://yanlab.asu.edu/Resources.h
 * `-m\--molecule=[DNA|RNA]`
 the type of molecule contained in the input file (defaults to DNA)
 * `-t\--tiamat-version=[1|2]`
-the Tiamat version the input file was generated with. If you are not sure, it's probably 1, the default value
+the Tiamat version the input file was generated with. If you are not sure, it's probably 2, the default value
 * `-d\--default-base=[A|C|G|T|R|integer]`
-some of the bases generated by Tiamat has no associated type. By default, these bases are assigned a random type (either A, C, G or T). By setting this option the user can assign to these bases the same type. Since oxDNA can also use integer numbers as types, these are also supported here
+some of the bases generated by Tiamat have no associated type. By default, these bases are assigned a random type (either A, C, G or T). By setting this option the user can assign to these bases the same type. Since oxDNA can also use integer numbers as types, these are also supported here
 * `-f\--print-force-file`
 also print a file containing the specifics for a oxDNA-compatible set of external forces that may be useful to relax the system
 

src/Tiamat_oxDNA.py

@@ -315,7 +315,7 @@ def print_usage():
         print >> sys.stderr, "\t[-t\--tiamat-version=1|2]"
         print >> sys.stderr, "\t[-t\--default-base=A|C|G|T|R|i (R = random, i = any integer)]"
         print >> sys.stderr, "\t[-f\--print-force-file]\n"
-        print >> sys.stderr, "\tThe defaults options are --molecule=DNA, --tiamat-version=1, --default-base=R"
+        print >> sys.stderr, "\tThe defaults options are --molecule=DNA, --tiamat-version=2, --default-base=R"
         exit(1)
 
 
@@ -332,7 +332,7 @@ def parse_options():
         "print_force_file" : False
     }
 
-    tiamat_version = 1
+    tiamat_version = 2
     try:
         import getopt
         args, positional_args = getopt.gnu_getopt(sys.argv[1:], shortArgs, longArgs)