From b35dc7fc5a532287e45ff6d5b436bc39032b9075 Mon Sep 17 00:00:00 2001 From: Gareth Aneurin Tribello Date: Fri, 31 Jan 2025 15:41:33 +0000 Subject: [PATCH] Fixed a couple of small things in manual pages for symfunc actions --- src/symfunc/CoordinationNumbers.cpp | 2 +- src/symfunc/Steinhardt.cpp | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/symfunc/CoordinationNumbers.cpp b/src/symfunc/CoordinationNumbers.cpp index d8cfd05292..1f2349dee1 100644 --- a/src/symfunc/CoordinationNumbers.cpp +++ b/src/symfunc/CoordinationNumbers.cpp @@ -56,7 +56,7 @@ one hundred atoms with themselves: ```plumed c: COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 -DUMPXYZ ATOMS=c ARG=c FILE=coords.xyz +DUMPATOMS ATOMS=c ARG=c FILE=coords.xyz ``` This input will produce an output file called coords that contains the coordination numbers of the 100 input atoms. The cutoff diff --git a/src/symfunc/Steinhardt.cpp b/src/symfunc/Steinhardt.cpp index e21e6b4376..4c2cb9daf1 100644 --- a/src/symfunc/Steinhardt.cpp +++ b/src/symfunc/Steinhardt.cpp @@ -53,9 +53,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e. -\f[ +$$ Q_1(i) = \sqrt{ \sum_{m=-1}^1 q_{1m}(i)^{*} q_{1m}(i) } -\f] +$$ This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities @@ -92,7 +92,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu ```plumed q1: Q1 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN -DUMPATOMS ATOMS=q1 ARG=q1_anorm FILE=q1.xyz +DUMPATOMS ATOMS=q1 ARG=q1 FILE=q1.xyz ``` */ @@ -119,9 +119,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e. -\f[ +$$ Q_3(i) = \sqrt{ \sum_{m=-3}^3 q_{3m}(i)^{*} q_{3m}(i) } -\f] +$$ This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities @@ -158,7 +158,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu ```plumed q3: Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN -DUMPATOMS ATOMS=q3 ARG=q3_anorm FILE=q3.xyz +DUMPATOMS ATOMS=q3 ARG=q3 FILE=q3.xyz ``` */ @@ -185,9 +185,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e. -\f[ +$$ Q_4(i) = \sqrt{ \sum_{m=-4}^4 q_{4m}(i)^{*} q_{4m}(i) } -\f] +$$ This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities @@ -224,7 +224,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu ```plumed q4: Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN -DUMPATOMS ATOMS=q4 ARG=q4_anorm FILE=q4.xyz +DUMPATOMS ATOMS=q4 ARG=q4 FILE=q4.xyz ``` */ @@ -251,9 +251,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e. -\f[ +$$ Q_6(i) = \sqrt{ \sum_{m=-6}^6 q_{6m}(i)^{*} q_{6m}(i) } -\f] +$$ This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities @@ -290,7 +290,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu ```plumed q6: Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN -DUMPATOMS ATOMS=q6 ARG=q6_anorm FILE=q6.xyz +DUMPATOMS ATOMS=q6 ARG=q6 FILE=q6.xyz ``` */