Merge release-4-5-patches into release-4-6

Conflicts:
	src/kernel/readir.c (trivial)

Change-Id: I6def10cca9a25c0587694ea77a5a6f7a43ca308d

diff --cc src/gmxlib/sfactor.c
Simple merge

diff --cc src/kernel/hizzie.c
Simple merge

diff --cc src/kernel/readir.c
index 3826994673b41e34b5487fdd8d7a585edca4707e,dc439ad0030a397169e554c4dd59ca01ce3c41b2..e22db5cacfcabd901c8917e73a0afa9604f3dd9b
--- 1/src/kernel/readir.c
--- 2/src/kernel/readir.c
+++ b/src/kernel/readir.c
@@@ -1647,23 -937,23 +1647,23 @@@ void get_ir(const char *mdparin,const c
    EETYPE("DispCorr",    ir->eDispCorr,  edispc_names);
    CTYPE ("Extension of the potential lookup tables beyond the cut-off");
    RTYPE ("table-extension", ir->tabext, 1.0);
-   CTYPE ("Seperate tables between energy group pairs");
+   CTYPE ("Separate tables between energy group pairs");
 -  STYPE ("energygrp_table", egptable,   NULL);
 +  STYPE ("energygrp-table", egptable,   NULL);
    CTYPE ("Spacing for the PME/PPPM FFT grid");
 -  RTYPE ("fourierspacing", opts->fourierspacing,0.12);
 +  RTYPE ("fourierspacing", ir->fourier_spacing,0.12);
    CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
 -  ITYPE ("fourier_nx",  ir->nkx,         0);
 -  ITYPE ("fourier_ny",  ir->nky,         0);
 -  ITYPE ("fourier_nz",  ir->nkz,         0);
 +  ITYPE ("fourier-nx",  ir->nkx,         0);
 +  ITYPE ("fourier-ny",  ir->nky,         0);
 +  ITYPE ("fourier-nz",  ir->nkz,         0);
    CTYPE ("EWALD/PME/PPPM parameters");
 -  ITYPE ("pme_order",   ir->pme_order,   4);
 -  RTYPE ("ewald_rtol",  ir->ewald_rtol, 0.00001);
 -  EETYPE("ewald_geometry", ir->ewald_geometry, eewg_names);
 -  RTYPE ("epsilon_surface", ir->epsilon_surface, 0.0);
 -  EETYPE("optimize_fft",ir->bOptFFT,  yesno_names);
 +  ITYPE ("pme-order",   ir->pme_order,   4);
 +  RTYPE ("ewald-rtol",  ir->ewald_rtol, 0.00001);
 +  EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
 +  RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
 +  EETYPE("optimize-fft",ir->bOptFFT,  yesno_names);
  
    CCTYPE("IMPLICIT SOLVENT ALGORITHM");
 -  EETYPE("implicit_solvent", ir->implicit_solvent, eis_names);
 +  EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
        
    CCTYPE ("GENERALIZED BORN ELECTROSTATICS"); 
    CTYPE ("Algorithm for calculating Born radii");

diff --cc src/tools/gmx_genpr.c
Simple merge

diff --cc src/tools/gmx_rmsf.c
Simple merge