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evcorr


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usage:c = evcorr(a,b)


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usage:c = evcorr(a,b)



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molsim


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 usage molsim(action, specifier, arg1, arg2, ...)

 See 'tutorial.pdf' reference quick sheet (installed in package directory under doc/). 




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 usage molsim(action, specifier, arg1, arg2, ...)



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molsim_calccf


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 Usage: css = molsim_calccf(a, b, nblocks)
  
 Calculates (directly) the correlation function between data arrays a and b
  
 Arguments: 
   - a and b; data arrays
   - nblocks; Number of blocks the arrays are divided into (default 1)

 Output
	 - The correlations function




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 Usage: css = molsim_calccf(a, b, nblocks)
  
 Calculates (directly) the cor...



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molsim_calcmsd


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 usage:  [msd scatt time waves] = molsim_msd(ptype, numbwave, haveCrossing (bool), maximum config file index)

 Calculates the mean square distance from configuration files molsim_%05d.xyz and crossing files
 crossings-%05d.dat. If the later does not exist an attempt to estimate the particles' box crossings.
 



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 usage:  [msd scatt time waves] = molsim_msd(ptype, numbwave, haveCrossing (...



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molsim_calcrdf


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 Usage: [radius, radial] = molsim_calcrdf(ptypes, npoints)

 Calculates the radial distribution function from configuration 
 files molsim-%05d.xyz.  

   Arguments: 
      - ptypes; pair particle types (default 'AA');
      - npoints; Resolution (default 100);

   Output: 
      - Radius
      - The radial distribution function (non-normalised)




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 Usage: [radius, radial] = molsim_calcrdf(ptypes, npoints)



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molsim_calcstrct


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 Usage: s = molsim_calcstrct(g, r, k, rho0)
  
 Calculates the structure factor from the radial distribution function
  
 Arguments: 
   - g Radial distribution function
   - r Radial coordinate
   - k Wave vector
   - rho0 System density (default 1)

 Output
	 - The structure factor




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 Usage: s = molsim_calcstrct(g, r, k, rho0)
  
 Calculates the structure fac...



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molsim_gh_transverse


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 usage: retval = molsim_gh_transverse(sample_time, sample_tvacf, wavectors, temperature, density, fitstrct)
 Input: 
 sample_time: Time span of the correlation function
 sample_tmacf: The tmacf - rows -> time, columns -> the different wavevectors
 temperature: System temperature
 density: System density
 fitstrct: Structure with elements
		verbose: true or false
		Cjj_fun: fitting for tmacf - values 'classic' or 'maxwell' (classical NS or Maxwell type) 
		Cjj_param0: Init params for Cjj fitting - scalar for 'classic' 2-vector for 'maxwell'
      etak_param0: Init params for etak fitting - 3-vector
      omega: Frequencies in the Fourier-Laplace representation




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 usage: retval = molsim_gh_transverse(sample_time, sample_tvacf, wavectors, ...



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molsim_rdf


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--- [rdf, r] = molsim_rdf(rdf pair types, particle positions, particle types, box dimensions, lvec) 


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--- [rdf, r] = molsim_rdf(rdf pair types, particle positions, particle types,...



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molsim_readxyz


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 -- [npart, types, pos, vel, mass, charge, lbox]  = molsim_readxyz(filename, option)
 -- [npart, types, pos] = molsim_readxyz(filename)
 
 Reads xyz-format configuration file

 Inputs: 

 filename - the xyz-file (string)
 option  - specific xyz format file option (default 'simple')
           *if option is 'simple' the following format is assumed
                type x-position y-position z-position

           *if option is 'sep' the seplib xyz format is assumed.

 Outputs:

 npart, types, pos - numb. particles (scalar), particle types (vector), position (npart x 3 matrix) 
 
 vel, mass, charge lbox - velocities (npart x 3 matrix), masses (vector), charges (vector), box dimensions (vector)  




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 -- [npart, types, pos, vel, mass, charge, lbox]  = molsim_readxyz(filename,...



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molsim_runlj


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 molsim_runlj: Simple Lennard-Jones simulation

 Test: 




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 molsim_runlj: Simple Lennard-Jones simulation



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molsim_viscprop


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undocumented function: retval = molsim_viscprop (_time, stress, nblocks = 10, volume = 1, temp = 1, _verbose = true, omega = logspace (-2, 1))


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undocumented function: retval = molsim_viscprop (_time, stress, nblocks = 10,...



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molslitconf


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 usage; molslitconf(xyzFile, topFile, densFluid, height, numberMol, atype, lbond, bcc)
	
  xyzFile: Single molecule xyz file
  topFile: Single molecule topology file
  densFluid: Desired molecular fluid density
  height: Desired slitpore height (confining direction)
  numberMol: Number of molecules 
  atype: Atomic type (character in molecule) OPTIONAL - defaults to 'A'
  lbond: Bond length OPTIONAL - defaults to 1.0
  bcc: set body centered crystal - default set to true 




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 usage; molslitconf(xyzFile, topFile, densFluid, height, numberMol, atype, l...





