system.cfg

system:
{
	/* define some system parameters */
	dimensions = [ 10.0, 10.0, 20.0 ];
	periodic = true;
	timesteps = 2000;
	temp-output = "temp.dat";

files:
	{
		prmtop = "prmtop";
		mdcrd = "mdcrd";
		mdvel = "mdvel";
		xyzfile = "xyz";
		wanniers = "wanniers";
		gmx-grofile = "grofile";
		gmx-trrfile = "trrfile";
		gmx-xtcfile = "xtcfile";
	};

};

analysis:
{
	reference-axis = 1;										// X = 0, Y = 1, Z = 2
	reference-vector = [ 0.0, 1.0, 0.0 ];	// major axis for analyses
	position-range = [ 0.0, 120.0 ];		// sets posmin and posmax for the system analysis
	PBC-flip = 20.0;										// used for centering system analysis if needed for periodic boundary conditions

	angle-range = [ -1.0, 1.0 ];

	restart-time = 0;
	output-frequency = 100;
	averaging = FALSE;

	reference-molecule-id = 90;

test:
	{
		filename = "dipole.dat";
		min = 0.0;
		max = 6.0;
		res = 0.01;
	};

resolution:
	{
		position = 0.1;
		angle = 0.01;
		frequency = 1.0;
	};

sfg:
	{
		filename = "na2so4-test-divide-sqrt-dpdp-2pixw-sfg.dat";
		polarization = [ 0, 2, 1 ];
		interface-low = 15.0;
		interface-high = 40.0;
	};

morita2002:
	{
		number-of-analysis-waters = 300;
	};

rdf:
	{
		filename = "RDF-analysis.dat";
		rdf-type = 1;
		minimum = 0.0;
		maximum = 20.0;
		resolution = 0.1;
		position-cutoff-low = 23.0;
		position-cutoff-high = 55.0;
		position-resolution = 1.0;
		atom-pairs = ( ("O", "C"), ("C", "H1"), ("O", "Cl1") );
	};

angle-bond-histogram:
	{
		filename = "2D-Angle-Position-Histogram.Bisector.dat";
		bondlength-min = 0.80;
		bondlength-max = 1.40;
		angle-min = 60.0;
		angle-max = 130.0;
		number-of-bins = 100;
	};

charge:
	{
		filename = "system-charge.dat";
	};

efield:
	{
		filename = "efield.dat";
		position-cutoff-low = 15.0;
		position-cutoff-high = 55.0;
	};

density:
	{
		filename = "atomic-density-test.dat";
		atom-names = ( "O", "H1", "H2" );
	};
};