From e4f73b3e58f62ed09f5217fc03b92294d2834571 Mon Sep 17 00:00:00 2001
From: ygutier2 <yair.fosado@ed.ac.uk>
Date: Sat, 2 Jul 2022 20:54:01 +0100
Subject: [PATCH] final changes commit
---
.DS_Store | Bin 6148 -> 6148 bytes
1_DNAModels/.DS_Store | Bin 6148 -> 6148 bytes
1_DNAModels/3_oxDNA/.DS_Store | Bin 0 -> 6148 bytes
1_DNAModels/3_oxDNA/oxDNA1/bash.run.sh | 10 +++++-----
1_DNAModels/3_oxDNA/oxDNA2/bash.run.sh | 10 +++++-----
2_Melting/.DS_Store | Bin 6148 -> 6148 bytes
2_Melting/1_linear/.DS_Store | Bin 0 -> 6148 bytes
.../1_linear/2_equilibration/bash.run.sh | 10 +++++-----
3_oxView/.DS_Store | Bin 0 -> 6148 bytes
README.md | 16 ++++++++++------
10 files changed, 25 insertions(+), 21 deletions(-)
create mode 100644 1_DNAModels/3_oxDNA/.DS_Store
create mode 100644 2_Melting/1_linear/.DS_Store
create mode 100644 3_oxView/.DS_Store
diff --git a/.DS_Store b/.DS_Store
index 567e7e8b7b8826f5327abfb6d2c9abdab530b001..2bf1a94da2fd050f3bc5e6fc6a31bb34207765f9 100644
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diff --git a/1_DNAModels/.DS_Store b/1_DNAModels/.DS_Store
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diff --git a/1_DNAModels/3_oxDNA/.DS_Store b/1_DNAModels/3_oxDNA/.DS_Store
new file mode 100644
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diff --git a/1_DNAModels/3_oxDNA/oxDNA1/bash.run.sh b/1_DNAModels/3_oxDNA/oxDNA1/bash.run.sh
index af0f417..bdb973a 100755
--- a/1_DNAModels/3_oxDNA/oxDNA1/bash.run.sh
+++ b/1_DNAModels/3_oxDNA/oxDNA1/bash.run.sh
@@ -1,7 +1,10 @@
#!/bin/bash
+#Current working directory variable
+cwd=`pwd`
#Location of the LAMMPS executables
-LAMMPSparallel="/Disk/ds-sopa-personal/ygutier2/SoftwareMD/lammps-29Sep2021/exec/lmp_mpi_29Sep2021"
+LAMMPS="${cwd}/../../../lmp_serial_29Sept2021"
+LAMMPSparallel="${cwd}/../../../lmp_mpi_29Sept2021"
#Name of the lammps script to run
lscript="oxDNA.commands"
@@ -14,9 +17,6 @@ intl="initial_configuration_N${nbp}_phi0.6"
#Number of cpu's to use in the simulation
ncpu=1
-
-#Current working directory variable
-cwd=`pwd`
mkdir -p REP1
cd REP1
@@ -30,4 +30,4 @@ cwd=`pwd`
echo "variable seed equal ${r1}" > parameters.dat
echo "variable seed1 equal ${r2}" >> parameters.dat
- mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
+ mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
\ No newline at end of file
diff --git a/1_DNAModels/3_oxDNA/oxDNA2/bash.run.sh b/1_DNAModels/3_oxDNA/oxDNA2/bash.run.sh
index af0f417..bdb973a 100755
--- a/1_DNAModels/3_oxDNA/oxDNA2/bash.run.sh
+++ b/1_DNAModels/3_oxDNA/oxDNA2/bash.run.sh
@@ -1,7 +1,10 @@
#!/bin/bash
+#Current working directory variable
+cwd=`pwd`
#Location of the LAMMPS executables
-LAMMPSparallel="/Disk/ds-sopa-personal/ygutier2/SoftwareMD/lammps-29Sep2021/exec/lmp_mpi_29Sep2021"
+LAMMPS="${cwd}/../../../lmp_serial_29Sept2021"
+LAMMPSparallel="${cwd}/../../../lmp_mpi_29Sept2021"
#Name of the lammps script to run
lscript="oxDNA.commands"
@@ -14,9 +17,6 @@ intl="initial_configuration_N${nbp}_phi0.6"
#Number of cpu's to use in the simulation
ncpu=1
-
-#Current working directory variable
-cwd=`pwd`
mkdir -p REP1
cd REP1
@@ -30,4 +30,4 @@ cwd=`pwd`
echo "variable seed equal ${r1}" > parameters.dat
echo "variable seed1 equal ${r2}" >> parameters.dat
- mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
+ mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
\ No newline at end of file
diff --git a/2_Melting/.DS_Store b/2_Melting/.DS_Store
index 11fc59f2f1cb5fae362eb1bed446a7e75aef2edc..71d769745b438cda857696f5da0e02d7058e4898 100644
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diff --git a/2_Melting/1_linear/.DS_Store b/2_Melting/1_linear/.DS_Store
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diff --git a/2_Melting/1_linear/2_equilibration/bash.run.sh b/2_Melting/1_linear/2_equilibration/bash.run.sh
index 9bf467a..bcfc972 100755
--- a/2_Melting/1_linear/2_equilibration/bash.run.sh
+++ b/2_Melting/1_linear/2_equilibration/bash.run.sh
@@ -1,7 +1,10 @@
#!/bin/bash
+#Current working directory variable
+cwd=`pwd`
#Location of the LAMMPS executables
-LAMMPSparallel="/Disk/ds-sopa-personal/ygutier2/SoftwareMD/lammps-29Sep2021/exec/lmp_mpi_29Sep2021"
+LAMMPS="${cwd}/../../../lmp_serial_29Sept2021"
+LAMMPSparallel="${cwd}/../../../lmp_mpi_29Sept2021"
#Name of the lammps script to run
lscript="oxDNA.commands"
@@ -14,9 +17,6 @@ intl="linear.N${nbp}.lammps"
#Number of cpu's to use in the simulation
ncpu=1
-
-#Current working directory variable
-cwd=`pwd`
mkdir -p REP1
cd REP1
@@ -30,4 +30,4 @@ cwd=`pwd`
echo "variable seed equal ${r1}" > parameters.dat
echo "variable seed1 equal ${r2}" >> parameters.dat
- mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
+ mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
\ No newline at end of file
diff --git a/3_oxView/.DS_Store b/3_oxView/.DS_Store
new file mode 100644
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diff --git a/README.md b/README.md
index 1b9f420..664c208 100755
--- a/README.md
+++ b/README.md
@@ -10,7 +10,11 @@ Furtheremore, we will discuss how to:
4. Analyse the output from simulations.
## Requirements
-In this section you will find the software neccessary for this tutorial and instructions on how to install it.
+In this section you will find the software neccessary for this tutorial and instructions on how to install it. The tutorial assumes that a LAMMPS executable called **lmp\_mpi\_29Sep2021** exist into this folder (see below for installation).
+
+Also, we recomend to create an alias for ovito. To this end, open a terminal into your home directory and type *vim bash.rc*. Then add the line:
+
+alias=ovito
### Git
Git is a distributed version control software. This is, a way to save changes over time without overwriting previous versions. The instructions to install it in *Windows, Linux and Mac* can be found in the following [Link](https://github.com/git-guides/install-git).
@@ -23,7 +27,7 @@ In this tutorial we will implement simulations of DNA using [oxDNA](https://dna.
One important feature of the oxDNA model is that [recently](https://link.springer.com/article/10.1140/epje/i2018-11669-8) it was implemented as a package that can be build into LAMMPS. Here, I mentioned the general steps on how to build LAMMPS with this package (assuming that you are using a computer with either macOS or linux-OS such as Ubuntu). For different operating systems please follow instructions [here](https://docs.lammps.org/Install.html).
-We will work with the current stable release of LAMMPS (**29-September-2021**) that can be installed in the following way: Assuming that you have a terminal located in the **home** directory, you have to type:
+We will work with the current stable release of LAMMPS (**29-Sept-2021**) that can be installed in the following way: Assuming that you have a terminal located in the **home** directory, you have to type:
> git clone -b stable https://github.com/lammps/lammps.git mylammps
>
@@ -33,13 +37,13 @@ We will work with the current stable release of LAMMPS (**29-September-2021**) t
>
> cd ../
>
-> make yes-molecule yes-asphere yes-CG-DNA
+> make yes-molecule yes-asphere yes-CG-DNA yes-extra-molecule
>
-> make serial
+> make mpi
>
-> mv lmp\_serial ~/lmp\_serial_29Sep2021
+> mv lmp\_mpi ~/lmp\_mpi_29Sep2021
-With this, an executable with the name **lmp\_serial\_29Sep2021** shoul have been created in your home directory (*~/*).
+With this, an executable with the name **lmp\_mpi\_29Sep2021** shoul have been created in your home directory (*~/*). Copy the executable into this folder, where you downloaded the tutorial.
### Ovito
In the tutorial we will learn how to visualize the output generated from simulations. To this end, we will use [Ovito](https://www.ovito.org) a visualization tool that can deal with aspherical particles. This is necessary to capture the planarity of bases in a nucleotide.
--
GitLab