usage

README.md

@@ -12,6 +12,43 @@ Features
 - Multidimensional
 - Unit tested
 
+Usage
+---
+wham has a convenient command line interface. You can see all options with
+```wham -h```:
+
+To run the two dimensional example (simulation of dialanine phi and psi angle):
+```bash
+wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example/2d/metadata.dat       
+> Supplied WHAM options: Metadata=example/2d/metadata.dat, hist_min=[-3.14, -3.14], hist_max=[3.14, 3.14], bins=[100, 100] verbose=false, tolerance=0.000001, iterations=100000, temperature=300, cyclic=true
+> Reading input files.
+> 625 windows, 624262 datapoints
+> Iteration 10: dF=0.389367172324539
+> Iteration 20: dF=0.21450559607810152
+(...)
+> Iteration 620: dF=0.0000005800554892309461
+> Iteration 630: dF=0.00000047424278621817084
+> Finished. Dumping final PMF
+(... pmf dump ...)
+
+```
+After convergence, final bias offsets (F) and the free energy will be dumped to stdout and the output file is written.
+
+
+The output file contains the free energy and probability for each bin. Probabilities are normalized to sum to P=1.0 and
+the smallest free energy is set to 0 (with other free energies based on that).
+```
+#coord1         coord2       Free Energy Probability
+-3.109590    	-3.109590    10.330312   0.000095
+-3.046770    	-3.109590    8.907360    0.000168
+-2.983950    	-3.109590    7.431969    0.000303
+-2.921130    	-3.109590    6.170882    0.000502
+-2.858310    	-3.109590    4.982956    0.000809
+-2.795490    	-3.109590    3.584741    0.001417
+-2.732670    	-3.109590    3.025337    0.001773
+(...)
+```
+
 Examples
 ---
 The example folder contains input and output files for two simple test systems: