Update README

README

-/==========================================================\
-| Atomic Resolution Brownian Dynamics (ARBD) - beta Oct 19 |
-\==========================================================/
-
-Brownian dynamics (BD) simulation is method for studying biomolecules, ions, and
-nanomaterials that balances detail with computational efficiency.
-
-ARBD supports tabulated non-bonded and bonded interactions between BD
-particles that can also be influenced by grid-specified
-potentials. Uniquely, ARBD also allows grid-specified densities and
-potentials to be associated with rigid body particles that rotate and
-translate to represent larger molecules. Most importantly, the code is
-designed to run quickly on modern NVIDIA GPUs.
-
-ARBD is a rewrite of the BrownianMover code, moving almost all computations to
-the GPU and enabling grid-specified particle models. Please be aware that ARBD
-is being actively developed and is offered without warranty.
-
-
-/==========\
-| Building |
-\==========/
-
-To build, please run `make' in the src directory.
-
-If your CUDA toolkit is installed in a nonstandard location, you may specify
-that location using the CUDA_PATH environment variable. For example:
-make CUDA_PATH=/nonstandard/path/to/cuda
-
-Note that ARBD has been developed using CUDA-8.0 and targets NVIDIA GPUs featuring
-6.0 compute capability. The code should work with devices with compute capability >=2.0,
-but there are no guarantees.
-
-Older versions of CUDA are not compatible with SM 6.0, so you may need to change
-the SMS variable in the makefile, or specify it as an argument to make.
-
-
-/==============\
-| Installation |
-\==============/
-
-Please explore the examples in the 'tests' directory.
-
-For example, try the following commands:
-
-cd tests/argon-small
-mkdir output
-../../src/arbd BrownDyn.bd output/BrownDyn > output/BrownDyn.log
-
-You may use the '-g n' option to specify the n-th GPU on your machine, counting from 0.
-
-If you fail to compile and link the applications, we recommend running
-`make clean` to remove object files. Sometimes we have encountered
-CUDA related errors in binaries built in a "dirty" environment.
-
-
-/========\
-| Citing |
-\========/
-
-If you publish results obtained using ARBD, please cite the following manuscripts:
-
-"DNA base-calling from a nanopore using a Viterbi algorithm"
-Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev
-Biophys J 102(10) L37-9 (2012)
-
-"Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics"
-Jeffrey Comer and Aleksei Aksimentiev.
-J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
-
-"Atoms-to-microns model for small solute transport through sticky nanochannels"
-Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev
-Lab Chip 11(22) 3766-73 (2011)
-
-
-/=========\
-| Authors |
-\=========/
-
-ARBD is developed by the Aksimentiev group (http://bionano.physics.illinois.edu)
-as a part of the NIH Center for Macromolecular Modeling and Bioinformatics
-(http://www.ks.uiuc.edu/).
-
-Please direct questions or problems to Chris.
-
-Christopher Maffeo <cmaffeo2@illinois.edu>
-Han-yi Chao
-Jeffrey Comer
-Max Belkin
-Emmanual Guzman
-Justin Dufresne
-Terrance Howard
-
-
-/====================\
-| Outstanding issues |
-\====================/
-
--- Not implemented --
-
-* There are no checks to ensure that pairlists are recalculated before
-  particles further than the pairlist distance move to within the
-  cutoff
-
--- Bugs --
-
-* A large amount of GPU memory for pairlists is allocated statically,
-  which may cause out-of-memory crashes in older hardware
-
-* If the number of pairs in the system exceeds the length of the array
-  allocated for pairlists, the non-bonded kernel will try to access
-  forbidden regions of memory, causing a crash

README.md

+# Atomic Resolution Brownian Dynamics (ARBD 2.0-alpha)
+
+Brownian dynamics (BD) simulation is method for studying biomolecules,
+ions, and nanomaterials that balances detail with computational
+efficiency.
+
+This development branch of ARBD has the aim of scaling ARBD up to
+larger systems and accelerating to the hardware limits, while making
+it easier to maintain diverse features. In particular we are seeking
+speed and good scaling on multi-GPU clusters.
+
+## Building
+
+### Dependencies
+
+Linux workstation with CUDA-compatible GPU (minimum 3.5 compute capability)
+  - CMake >= 3.9
+  - gcc >= 4.9
+  - cuda >= 9.0  (> 11.5 recommended)
+
+### Build process
+
+From the root arbd directory (where this README is found), run:
+```
+## Determine the compute capability of your CUDA-enabled graphics card
+export CMAKE_CUDA_ARCHITECTURES="35;50;75;80"   ;# especially important for CMake < 3.24.0
+## export CUDA_INCLUDE_DIRS="$CUDA_HOME/include" ;# optionally be explicit about cuda include paths; usually not needed
+cmake -S src -B build &&
+(
+  cd build
+  make -j
+)
+```
+
+If your CUDA toolkit is installed in a nonstandard location that CMake
+is unable to find, you may provide use the environement variable
+`CMAKE_CUDA_COMPILER` to specify the path to nvcc. You may also find
+it neccesary to set the environment variable `CUDA_INCLUDE_DIRS` if
+compilation fails due to the compiler being unable to find <cuda.h>.
+
+Note that ARBD has been developed using CUDA-9.0 and targets NVIDIA
+GPUs featuring 6.0 compute capability. The code should work with
+devices with compute capability >=2.0, but there are no guarantees.
+
+## Authors
+
+ARBD is developed by the Aksimentiev group
+(http://bionano.physics.illinois.edu).
+
+Please direct questions or problems to Chris.
+
+- Christopher Maffeo <cmaffeo2@illinois.edu>
+- Han-yi Chao