From 31bc9388667fa0d452a4fb0f5d793ec6dc42653b Mon Sep 17 00:00:00 2001
From: Martin Schroschk <martin.schroschk@tu-dresden.de>
Date: Tue, 29 Jun 2021 14:31:56 +0200
Subject: [PATCH] Fix checks

---
 .../docs/software/NanoscaleSimulations.md     | 329 ++++++++++--------
 1 file changed, 177 insertions(+), 152 deletions(-)

diff --git a/doc.zih.tu-dresden.de/docs/software/NanoscaleSimulations.md b/doc.zih.tu-dresden.de/docs/software/NanoscaleSimulations.md
index 004cc0566..1d5d2a98f 100644
--- a/doc.zih.tu-dresden.de/docs/software/NanoscaleSimulations.md
+++ b/doc.zih.tu-dresden.de/docs/software/NanoscaleSimulations.md
@@ -17,200 +17,225 @@
 
 ## NAMD
 
-[NAMD](http://www.ks.uiuc.edu/Research/namd) is a parallel molecular
-dynamics code designed for high-performance simulation of large
-biomolecular systems.
-
-The current version in modenv/scs5 can be started with srun as usual.
-
-Note that the old version from modenv/classic does not use MPI but
-rather uses Infiniband directly. Therefore, you cannot not use
-srun/mpirun to spawn the processes but have to use the supplied
-"charmrun" command instead. Also, since this is batch system agnostic,
-it has no possiblity of knowing which nodes are reserved for it use, so
-if you want it to run on more than node, you have to create a hostlist
-file and feed it to charmrun via the parameter "++nodelist". Otherwise,
-all processes will be launched on the same node (localhost) and the
-other nodes remain unused.
-
-You can use the following snippet in your batch file to create a
-hostlist file:
-
-    export NODELISTFILE="/tmp/slurm.nodelist.$SLURM_JOB_ID"
-    for LINE in `scontrol show hostname $SLURM_JOB_NODELIST` ; do
-      echo "host $LINE" >> $NODELISTFILE ;
-    done
-
-    # launch NAMD processes. Note that the environment variable $SLURM_NTASKS is only available if you have
-    # used the -n|--ntasks parameter. Otherwise, you have to specify the number of processes manually, e.g. +p64
-    charmrun +p$SLURM_NTASKS ++nodelist $NODELISTFILE $NAMD inputfile.namd
-
-    # clean up afterwards:
-    test -f $NODELISTFILE && rm -f $NODELISTFILE
-
-The current version 2.7b1 of NAMD runs much faster than 2.6. -
-Especially on the SGI Altix. Since the parallel performance strongly
-depends on the size of the given problem one cannot give a general
-advice for the optimum number of CPUs to use. (Please check this by
-running NAMD with your molecules and just a few time steps.)
-
-Any published work which utilizes NAMD shall include the following
-reference: \<br /> *James C. Phillips, Rosemary Braun, Wei Wang, James
-Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D.
-Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics
-with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005.*
-
-Electronic documents will include a direct link to the official NAMD
-page at <http://www.ks.uiuc.edu/Research/namd/>
+[NAMD](http://www.ks.uiuc.edu/Research/namd) is a parallel molecular dynamics code designed for
+high-performance simulation of large biomolecular systems.
 
-## Gaussian
+The current version in modenv/scs5 can be started with `srun` as usual.
 
-Starting from the basic laws of quantum mechanics,
-[Gaussian](http://www.gaussian.com) predicts the energies, molecular
-structures, and vibrational frequencies of molecular systems, along with
-numerous molecular properties derived from these basic computation
-types. It can be used to study molecules and reactions under a wide
-range of conditions, including both stable species and compounds which
-are difficult or impossible to observe experimentally such as
-short-lived intermediates and transition structures.
+Note that the old version from modenv/classic does not use MPI but rather uses Infiniband directly.
+Therefore, you cannot not use srun/mpirun to spawn the processes but have to use the supplied
+"charmrun" command instead. Also, since this is batch system agnostic, it has no possiblity of
+knowing which nodes are reserved for it use, so if you want it to run on more than node, you have to
+create a hostlist file and feed it to charmrun via the parameter "++nodelist". Otherwise, all
+processes will be launched on the same node (localhost) and the other nodes remain unused.
 
-With `module load gaussian` (or `gaussian/g09`) a number of environment
-variables are set according to the needs of Gaussian. Please, set the
-directory for temporary data (GAUSS_SCRDIR) manually to somewhere below
-\<span>/scratch (you get the path, when you generated a workspace for
-your calculation)\<br />\</span>
+You can use the following snippet in your batch file to create a hostlist file:
 
-This is a small example, kindly provide by Arno Schneeweis (Inst. fr
-Angewandte Physik). You need a batch file - for example called
-"mybatch.sh" with the following content:
+```Bash
+export NODELISTFILE="/tmp/slurm.nodelist.$SLURM_JOB_ID"
+for LINE in `scontrol show hostname $SLURM_JOB_NODELIST` ; do
+  echo "host $LINE" >> $NODELISTFILE ;
+done
 
-    #!/bin/bash<br />#SBATCH --nodes=1<br />#SBATCH --ntasks-per-node=4    # this number of CPU's has to match with the %nproc in the inputfile<br />#SBATCH --mem=4000<br />#SBATCH --time=00:10:00        # hh:mm:ss<br />#SBATCH --mail-type=END,FAIL<br />#SBATCH --mail-user=vorname.nachname@tu-dresden.de<br />#SBATCH -A ...your_projectname...   <br /><br />#### make available the access to Gaussian 16<br />module load modenv/classic<br />module load gaussian/g16_avx2<br />export GAUSS_SCRDIR=...path_to_the_Workspace_that_you_generated_before...<br />g16 &lt; my_input.com &gt; my_output.out 
+# launch NAMD processes. Note that the environment variable $SLURM_NTASKS is only available if you have
+# used the -n|--ntasks parameter. Otherwise, you have to specify the number of processes manually, e.g. +p64
+charmrun +p$SLURM_NTASKS ++nodelist $NODELISTFILE $NAMD inputfile.namd
 
-*As example the input for gaussian could be this my_input.com:\<br />*
+# clean up afterwards:
+test -f $NODELISTFILE && rm -f $NODELISTFILE
+```
 
-    %mem=4GB<br />%nproc=4<br />#P B3LYP/6-31G* opt<br /><br />Toluol<br /><br />0 1<br />C    1.108640   0.464239  -0.122043<br />C    1.643340  -0.780361   0.210457<br />C    0.794940  -1.850561   0.494257<br />C   -0.588060  -1.676061   0.445657<br />C   -1.122760  -0.431461   0.113257<br />C   -0.274360   0.638739  -0.170643<br />C   -0.848171   1.974558  -0.527484<br />H    1.777668   1.308198  -0.345947<br />H    2.734028  -0.917929   0.248871<br />H    1.216572  -2.832148   0.756392<br />H   -1.257085  -2.520043   0.669489<br />H   -2.213449  -0.293864   0.074993<br />H   -1.959605   1.917127  -0.513867<br />H   -0.507352   2.733596   0.211754<br />H   -0.504347   2.265972  -1.545144<br /><br />
+The current version 2.7b1 of NAMD runs much faster than 2.6. - Especially on the SGI Altix. Since
+the parallel performance strongly depends on the size of the given problem one cannot give a general
+advice for the optimum number of CPUs to use. (Please check this by running NAMD with your molecules
+and just a few time steps.)
 
-You have to start the job with command:
+Any published work which utilizes NAMD shall include the following reference:
 
-sbatch mybatch.sh
+*James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe
+Chipot, Robert D.  Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD.
+Journal of Computational Chemistry, 26:1781-1802, 2005.*
 
-## \<a name="gamess">\</a>GAMESS US
+Electronic documents will include a direct link to the official NAMD page at
+http://www.ks.uiuc.edu/Research/namd
 
-GAMESS is an ab-initio quantum mechanics program, which provides many
-methods for computation of the properties of molecular systems using
-standard quantum chemical methods. For a detailed description, please
-look at the [GAMESS home
-page](http://www.msg.ameslab.gov/GAMESS/GAMESS.html).
+## Gaussian
 
-For runs with Slurm, please use a script like this:
+Starting from the basic laws of quantum mechanics, [Gaussian](http://www.gaussian.com) predicts the
+energies, molecular structures, and vibrational frequencies of molecular systems, along with
+numerous molecular properties derived from these basic computation types. It can be used to study
+molecules and reactions under a wide range of conditions, including both stable species and
+compounds which are difficult or impossible to observe experimentally such as short-lived
+intermediates and transition structures.
+
+With `module load gaussian` (or `gaussian/g09`) a number of environment variables are set according
+to the needs of Gaussian. Please, set the directory for temporary data (GAUSS_SCRDIR) manually to
+somewhere below `/scratch` (you get the path, when you generated a workspace for your
+calculation).
+
+This is a small example, kindly provide by Arno Schneeweis (Inst. fr Angewandte Physik). You need a
+batch file - for example called "mybatch.sh" with the following content:
+
+```Bash
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4    # this number of CPU's has to match with the %nproc in the inputfile
+#SBATCH --mem=4000
+#SBATCH --time=00:10:00        # hh:mm:ss
+#SBATCH --mail-type=END,FAIL
+#SBATCH --mail-user=vorname.nachname@tu-dresden.de
+#SBATCH -A ...your_projectname...
+
+####
+make available the access to Gaussian 16
+module load modenv/classic
+module load gaussian/g16_avx2
+export GAUSS_SCRDIR=...path_to_the_Workspace_that_you_generated_before...
+g16 < my_input.com > my_output.out
+```
+
+*As example the input for gaussian could be this my_input.com:*
+
+```Bash
+%mem=4GB
+%nproc=4
+
+#P B3LYP/6-31G* opt
+
+Toluol
+
+0 1
+C    1.108640   0.464239  -0.122043
+C    1.643340  -0.780361   0.210457
+C    0.794940  -1.850561   0.494257
+C   -0.588060  -1.676061   0.445657
+C   -1.122760  -0.431461   0.113257
+C   -0.274360   0.638739  -0.170643
+C   -0.848171   1.974558  -0.527484
+H    1.777668   1.308198  -0.345947
+H    2.734028  -0.917929   0.248871
+H    1.216572  -2.832148   0.756392
+H   -1.257085  -2.520043   0.669489
+H   -2.213449  -0.293864   0.074993
+H   -1.959605   1.917127  -0.513867
+H   -0.507352   2.733596   0.211754
+H   -0.504347   2.265972  -1.545144
+```
 
-    #!/bin/bash<br />#SBATCH -t 120<br />#SBATCH -n 8<br />#SBATCH --ntasks-per-node=2<br /># you have to make sure that on each node runs an even number of tasks !!<br />#SBATCH --mem-per-cpu=1900<br />module load gamess<br />rungms.slurm cTT_M_025.inp /scratch/mark/gamess  <br />#                          the third parameter is the location of the scratch directory<br /> 
+You have to start the job with command:
 
-*GAMESS should be cited as:* M.W.Schmidt, K.K.Baldridge, J.A.Boatz,
-S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen,
-S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery, J.Comput.Chem. 14,
-1347-1363(1993).
+```Batch
+sbatch mybatch.sh
+```
+
+## GAMESS US
 
-## \<a name="lammps">\</a>LAMMPS
+GAMESS is an ab-initio quantum mechanics program, which provides many methods for computation of the
+properties of molecular systems using standard quantum chemical methods. For a detailed description,
+please look at the [GAMESS home page](http://www.msg.ameslab.gov/GAMESS/GAMESS.html).
 
-[LAMMPS](http://lammps.sandia.gov) is a classical molecular dynamics
-code that models an ensemble of particles in a liquid, solid, or gaseous
-state. It can model atomic, polymeric, biological, metallic, granular,
-and coarse-grained systems using a variety of force fields and boundary
-conditions. For examples of LAMMPS simulations, documentations, and more
-visit [LAMMPS sites](http://lammps.sandia.gov).
+For runs with Slurm, please use a script like this:
+
+```Bash
+#!/bin/bash
+#SBATCH -t 120
+#SBATCH -n 8
+#SBATCH --ntasks-per-node=2
+# you have to make sure that on each node runs an even number of tasks !!
+#SBATCH --mem-per-cpu=1900
+module load gamess
+rungms.slurm cTT_M_025.inp /scratch/mark/gamess
+#                          the third parameter is the location of the scratch directory
+```
+
+*GAMESS should be cited as:* M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon,
+J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery,
+J.Comput.Chem. 14, 1347-1363(1993).
+
+## LAMMPS
+
+[LAMMPS](http://lammps.sandia.gov) is a classical molecular dynamics code that models an ensemble of
+particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological,
+metallic, granular, and coarse-grained systems using a variety of force fields and boundary
+conditions. For examples of LAMMPS simulations, documentations, and more visit
+[LAMMPS sites](http://lammps.sandia.gov).
 
 ## ABINIT
 
-[ABINIT](http://www.abinit.org) is a package whose main program allows
-one to find the total energy, charge density and electronic structure of
-systems made of electrons and nuclei (molecules and periodic solids)
-within Density Functional Theory (DFT), using pseudopotentials and a
-planewave basis. ABINIT also includes options to optimize the geometry
-according to the DFT forces and stresses, or to perform molecular
-dynamics simulations using these forces, or to generate dynamical
-matrices, Born effective charges, and dielectric tensors. Excited states
-can be computed within the Time-Dependent Density Functional Theory (for
-molecules), or within Many-Body Perturbation Theory (the GW
-approximation).
+[ABINIT](http://www.abinit.org) is a package whose main program allows one to find the total energy,
+charge density and electronic structure of systems made of electrons and nuclei (molecules and
+periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave
+basis. ABINIT also includes options to optimize the geometry according to the DFT forces and
+stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical
+matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the
+Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory
+(the GW approximation).
 
 ## CP2K
 
-[CP2K](http://cp2k.berlios.de/) performs atomistic and molecular
-simulations of solid state, liquid, molecular and biological systems. It
-provides a general framework for different methods such as e.g. density
-functional theory (DFT) using a mixed Gaussian and plane waves approach
-(GPW), and classical pair and many-body potentials.
+[CP2K](http://cp2k.berlios.de/) performs atomistic and molecular simulations of solid state, liquid,
+molecular and biological systems. It provides a general framework for different methods such as e.g.
+density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical
+pair and many-body potentials.
 
 ## CPMD
 
-The CPMD code is a plane wave/pseudopotential implementation of Density
-Functional Theory, particularly designed for ab-initio molecular
-dynamics. For examples and documentations see [CPMD
-homepage](http://www.cpmd.org).
+The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory,
+particularly designed for ab-initio molecular dynamics. For examples and documentations see
+[CPMD homepage](http://www.cpmd.org).
 
 ## GROMACS
 
-GROMACS is a versatile package to perform molecular dynamics, i.e.
-simulate the Newtonian equations of motion for systems with hundreds to
-millions of particles. It is primarily designed for biochemical
-molecules like proteins, lipids and nucleic acids that have a lot of
-complicated bonded interactions, but since GROMACS is extremely fast at
-calculating the nonbonded interactions (that usually dominate
-simulations) many groups are also using it for research on
-non-biological systems, e.g. polymers.
+GROMACS is a versatile package to perform molecular dynamics, i.e.  simulate the Newtonian equations
+of motion for systems with hundreds to millions of particles. It is primarily designed for
+biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded
+interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that
+usually dominate simulations) many groups are also using it for research on non-biological systems,
+e.g. polymers.
 
 For documentations see [Gromacs homepage](http://www.gromacs.org/).
 
 ## ORCA
 
-ORCA is a flexible, efficient and easy-to-use general purpose tool for
-quantum chemistry with specific emphasis on spectroscopic properties of
-open-shell molecules. It features a wide variety of standard quantum
-chemical methods ranging from semiempirical methods to DFT to single-
-and multireference correlated ab initio methods. It can also treat
-environmental and relativistic effects.
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with
+specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of
+standard quantum chemical methods ranging from semiempirical methods to DFT to single- and
+multireference correlated ab initio methods. It can also treat environmental and relativistic
+effects.
 
-To run Orca jobs in parallel, you have to specify the number of
-processes in your input file (here for example 16 processes):
+To run Orca jobs in parallel, you have to specify the number of processes in your input file (here
+for example 16 processes):
 
-    %pal nprocs 16 end
+```Bash
+%pal nprocs 16 end
+```
 
-Note that Orca does the MPI process spawning itself, so you may not use
-"srun" to launch it in your batch file. Just set --ntasks to the same
-number as in your input file and call the "orca" executable directly.
-For parallel runs, it must be called with the full path:
+Note that Orca does the MPI process spawning itself, so you may not use "srun" to launch it in your
+batch file. Just set --ntasks to the same number as in your input file and call the "orca"
+executable directly.  For parallel runs, it must be called with the full path:
 
-    #!/bin/bash
-    #SBATCH --ntasks=16
-    #SBATCH --nodes=1
-    #SBATCH --mem-per-cpu=2000M
+```Bash
+#!/bin/bash #SBATCH --ntasks=16 #SBATCH --nodes=1 #SBATCH --mem-per-cpu=2000M
 
-    $ORCA_ROOT/orca example.inp
+$ORCA_ROOT/orca example.inp
+```
 
 ## Siesta
 
-Siesta (Spanish Initiative for Electronic Simulations with Thousands of
-Atoms) is both a method and its computer program implementation, to
-perform electronic structure calculations and ab initio molecular
-dynamics simulations of molecules and solids. <http://www.uam.es/siesta>
-
-In any paper or other academic publication containing results wholly or
-partially derived from the results of use of the SIESTA package, the
-following papers must be cited in the normal manner: 1 "Self-consistent
-order-N density-functional calculations for very large systems", P.
-Ordejon, E. Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53,
-R10441-10443 (1996). 1 "The SIESTA method for ab initio order-N
-materials simulation" J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J.
-Junquera, P. Ordejon, and D. Sanchez-Portal, J. Phys.: Condens. Matt.
-14, 2745-2779 (2002).
+Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and
+its computer program implementation, to perform electronic structure calculations and ab initio
+molecular dynamics simulations of molecules and solids. <http://www.uam.es/siesta>
+
+In any paper or other academic publication containing results wholly or partially derived from the
+results of use of the SIESTA package, the following papers must be cited in the normal manner: 1
+"Self-consistent order-N density-functional calculations for very large systems", P.  Ordejon, E.
+Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53, R10441-10443 (1996). 1 "The SIESTA method
+for ab initio order-N materials simulation" J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J.
+Junquera, P. Ordejon, and D. Sanchez-Portal, J. Phys.: Condens. Matt.  14, 2745-2779 (2002).
 
 ## VASP
 
-"VAMP/VASP is a package for performing ab-initio quantum-mechanical
-molecular dynamics (MD) using pseudopotentials and a plane wave basis
-set."
-[\[http://cms.mpi.univie.ac.at/vasp/ Official Site]([http://cms.mpi.univie.ac.at/vasp/ Official Site)\].
-It is installed on mars. If you are interested in using VASP on ZIH
-machines, please contact [Dr. Ulf
+"VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using
+pseudopotentials and a plane wave basis set." [VASP](https://www.vasp.at). It is installed on mars.
+If you are interested in using VASP on ZIH machines, please contact [Dr. Ulf
 Markwardt](http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/wir_ueber_uns/mitarbeiter/markwardt).
-- 
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