fix some more URLs

README

@@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
 run efficiently on parallel computers.  It was developed at Sandia
 National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
+under the terms of the GNU Public License (GPL) version 2.
 
 The primary author of the code is Steve Plimpton, who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:
@@ -37,14 +37,14 @@ tools                      pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://lammps.sandia.gov/doc/Manual.html         LAMMPS manual
-https://lammps.sandia.gov/doc/Intro.html          hi-level introduction
-https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
-https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
-https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
-https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
+https://docs.lammps.org/Manual.html         LAMMPS manual
+https://docs.lammps.org/Intro.html          hi-level introduction
+https://docs.lammps.org/Build.html          how to build LAMMPS
+https://docs.lammps.org/Run_head.html       how to run LAMMPS
+https://docs.lammps.org/Commands_all.html   Table of available commands
+https://docs.lammps.org/Library.html        LAMMPS library interfaces
+https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
+https://docs.lammps.org/Developer.html      LAMMPS developer info
 
 You can also create these doc pages locally:
 

bench/POTENTIALS/README

@@ -1,7 +1,7 @@
 These are input scripts used to run benchmark tests for many of the
 interatomic potentials in LAMMPS.  The results of running these
 scripts on different machines are shown on the Potentials section of
-the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 Examples are shown below of how to run these scripts.  Log files for
 running them on 1 and 4 processors of a Linux box are included in the

bench/README

@@ -2,7 +2,7 @@ LAMMPS benchmark problems
 
 This directory contains 5 benchmark problems which are discussed in
 the Benchmark section of the LAMMPS documentation, and on the
-Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 This directory also has several sub-directories:
 
@@ -11,7 +11,7 @@ KEPLER          benchmark scripts for GPU cluster with Kepler GPUs
 POTENTIALS      benchmarks scripts for various potentials in LAMMPS
 
 The results for all of these benchmarks are displayed and discussed on
-the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
+the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
 
 The remainder of this file refers to the 5 problems in the top-level
 of this directory and how to run them on CPUs, either in serial or

examples/ASPHERE/README

@@ -10,7 +10,7 @@ systems.  Some of the directories include a Python script, which can
 be used with the Pizza.py tool to create the data file, e.g. for
 collections of rigid bodies.
 
-The web site for Pizza.py is http://pizza.sandia.gov
+The web site for Pizza.py is https://pizza.sandia.gov
 
 For example, If you have Pizza.py installed you can type "pizza.py -f
 box.py", which creates the data.box data file in the box dir.
@@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir.
 If you uncomment the dump or dump image lines in the input scripts the
 runs will produce dump files or JPG images which you can view or
 animate.  See the Movies page of the LAMMPS web site
-(http://lammps.sandia.gov/movies.html), for animations of these
+(https://www.lammps.org/movies.html), for animations of these
 scripts.  Most were done using the dump image command.  A few were
 done using the gl tool in Pizza.py; the Pizza.py scripts that do the
 animation are given in the directory, e.g. as line.viz.py.

examples/README

@@ -37,7 +37,7 @@ produce dump snapshots of the running simulation in any of 3 formats.
 
 If you uncomment the dump command in the input script, a text dump
 file will be produced, which can be animated by various visualization
-programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD,
+programs (see https://www.lammps.org/viz.html) such as Ovito, VMD,
 or AtomEye.
 
 If you uncomment the dump image command in the input script, and

examples/VISCOSITY/README

@@ -28,7 +28,7 @@ minute or so and produce the accompanying log files and profile files
 (for velocity or momentum flux).
 
 See the Movies page of the LAMMPS web site
-(http://lammps.sandia.gov/movies.html), for animations of the NEMD
+(https://www.lammps.org/movies.html), for animations of the NEMD
 scripts, created using the dump image command.
 
 The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut =

examples/reax/HNS/README.txt

@@ -15,7 +15,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
   The file is read line by line looking for keywords to set up this run. 
   It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution.
   The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
-  More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
+  More information about each of the individual commands can be found online at www.lammps.org in the user manual section.
 
   *There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
   *The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
@@ -27,7 +27,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
     lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100
 
 2) LAMMPS Data file for crystalline HNS
-  This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov
+  This file matches the LAMMPS data format, more information about this data structure can be found at www.lammps.org
   
   This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z).
   The file contains eight molecules (2 unit cells).

lib/gpu/README

@@ -29,7 +29,7 @@ LAMMPS styles and neighbor list builds using CUDA, OpenCL, or ROCm HIP.
 Pair styles supported by this library are marked in the list of Pair style
 potentials with a "g". See the online version at:
 
-https://lammps.sandia.gov/doc/Commands_pair.html
+https://docs.lammps.org/Commands_pair.html
 
 In addition the (plain) pppm kspace style is supported as well.
 

python/examples/pylammps/README.md

@@ -4,7 +4,7 @@ This folder contains examples showcasing the usage of the PyLammps Python
 interface and Jupyter notebooks. To use this you will need LAMMPS compiled as
 a shared library and the LAMMPS Python package installed.
 
-An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a [PyLammps tutorial](https://lammps.sandia.gov/doc/Howto_pylammps.html).
+An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://docs.lammps.org/Python_install.html). There is also a [PyLammps tutorial](https://docs.lammps.org/Howto_pylammps.html).
 
 The following will show one way of creating a Python virtual environment
 which has both LAMMPS and its Python package installed:

tools/replica/README.md

@@ -1,6 +1,6 @@
 ## reorder_remd_traj
 
-LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories (implemented using the temper command) are arranged by replica, i.e., each trajectory is a continuous replica that records all the ups and downs in temperature. However, often the requirement is  that trajectories be continuous in temperature. This requires the LAMMPS REMD trajectories to be re-ordered, which LAMMPS does not do automatically. (see the discussion [here](https://lammps.sandia.gov/threads/msg60440.html)). The reorderLAMMPSREMD tool does exactly this in parallel (using MPI)
+LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories (implemented using the temper command) are arranged by replica, i.e., each trajectory is a continuous replica that records all the ups and downs in temperature. However, often the requirement is  that trajectories be continuous in temperature. This requires the LAMMPS REMD trajectories to be re-ordered, which LAMMPS does not do automatically. (see the discussion [here](https://www.lammps.org/threads/msg60440.html)). The reorderLAMMPSREMD tool does exactly this in parallel (using MPI)
 
 (Protein folding trajectories in [Sanyal, Mittal and Shell, JPC, 2019, 151(4), 044111](https://aip.scitation.org/doi/abs/10.1063/1.5108761) were ordered in temperature space using this tool)
 
@@ -49,7 +49,7 @@ So, when the dust settles,
   - `n` = replica number (0-15 in this case). Note: trajectories **must be in default LAMMPS format **(so stuff like dcd won't work)
 
 - You will also have a master LAMMPS log file (`logfn`) that contains the swap history of all the replicas
-  (for more details see [here](https://lammps.sandia.gov/doc/temper.html). Assume that this is called `log.peptide`
+  (for more details see [here](https://docs.lammps.org/temper.html). Assume that this is called `log.peptide`
 
 - Further you must have a txt file that numpy can read which stores all the temperature values (say this is called `temps.txt`)