diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt index 0c4c1f8dc29014ba47f819df72594e7af8d2e203..12abb139db736a1b21684bd22cc982d36bcd69b6 100644 --- a/CHANGES/Unreleased.txt +++ b/CHANGES/Unreleased.txt @@ -39,10 +39,10 @@ Changes from version 2.0 which are relevant for users: - \ref DUMPATOMS : PRECISION option to set number of digits in output file. - \ref GROUP : NDX_FILE and NDX_GROUP options to import atom lists from ndx (gromacs) files. - In many multicolvars, MIN and MAX options can be used. - - \ref HISTOGRAM: GRID_SPACING (alternative to GRID_BIN to set grid spacing), + - \ref HISTOGRAM : GRID_SPACING (alternative to GRID_BIN to set grid spacing), FREQUENCY and FREE-ENERGY flags in addition to standard probability density, additional option for KERNEL=NONE to accumulate standard histograms. - - \ref sum_hills: added options --spacing (alternative to --bin to set grid spacing) + - \ref sum_hills : added options --spacing (alternative to --bin to set grid spacing) and --setmintozero to translate the minimum of the output files to zero. - New features in MD patches (require repatch): - Gromacs 4.6.5 support \ref COMMITTOR analysis. diff --git a/src/crystallization/Q3.cpp b/src/crystallization/Q3.cpp index ed825b01d62b5468ff4aa65f04502be42bf1326d..8fcaa300cd26c4cf731a7f8046a1df96aae6b45a 100644 --- a/src/crystallization/Q3.cpp +++ b/src/crystallization/Q3.cpp @@ -126,7 +126,7 @@ quantity for each of the atoms in the system: where \f$q_{3m}(i)\f$ and \f$q_{3m}(j)\f$ are the 3rd order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterix denotes complex conjugation. The function -\f$\sigma( r_{ij} )\f$ is a \ref switching function that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set +\f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise. The sum in the numerator of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these adjacent atoms is correlated. diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp index 4680cd7a7a6b68ba31d7363103c577e323e7979e..5d1f1e2e79ba6f415b1b394cd35589077f01dfaf 100644 --- a/src/crystallization/Q4.cpp +++ b/src/crystallization/Q4.cpp @@ -126,7 +126,7 @@ quantity for each of the atoms in the system: where \f$q_{4m}(i)\f$ and \f$q_{4m}(j)\f$ are the 4th order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterix denotes complex conjugation. The function -\f$\sigma( r_{ij} )\f$ is a \ref switching function that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set +\f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise. The sum in the numerator of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these adjacent atoms is correlated. diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp index e81cd9bbfb1bc06f69a8bdeae249a5a67203a542..3687717e6d2fb7af8fbe539caf9681f1dd381a2b 100644 --- a/src/crystallization/Q6.cpp +++ b/src/crystallization/Q6.cpp @@ -126,7 +126,7 @@ quantity for each of the atoms in the system: where \f$q_{6m}(i)\f$ and \f$q_{6m}(j)\f$ are the 6th order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterix denotes complex conjugation. The function -\f$\sigma( r_{ij} )\f$ is a \ref switching function that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set +\f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$. The parameters of this function should be set so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise. The sum in the numerator of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these adjacent atoms is correlated.