diff --git a/examples/SPIN/gneb/README b/examples/SPIN/gneb/README index 6f5db6d388..9d43c775b6 100644 --- a/examples/SPIN/gneb/README +++ b/examples/SPIN/gneb/README @@ -8,3 +8,6 @@ Run those examples as: mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1 You should be able to use any number of replicas >= 3. + +In the interpolate/ directory, a c routine is provided to +interpolate the MEP. diff --git a/examples/SPIN/gneb/interpolate/README b/examples/SPIN/gneb/interpolate/README index d0f75226c5..5cfd267a86 100644 --- a/examples/SPIN/gneb/interpolate/README +++ b/examples/SPIN/gneb/interpolate/README @@ -1,7 +1,31 @@ Interpolate.x tries to perform a cubic polynomial interpolation -of the MEP found +of the MEP. Compile the program with: gcc interpolate.c -o interpolate.x -lm -lgsl +and then run it as: +./interpolate.x +Enter N-1 (with N the number of replica). +The program reads the "neb_init.dat", in which you need to +replace the current values by your GNEB outputs. + +Each line corresponds to a replica, and has to respectively +contain: + +Reac. coords /tab/ pot. energy /tab/ fm dot tangent /tab/ +geodesic dist to next replica + +All those information can be provided by the verbose output of +a neb/spin calculation + +The progam outputs the interpolation result, and the +interpolated MEP in "interpolation_result.dat". + +This code is a courtesy of Aleksei Ivanov, University of +Iceland. +For more explanation about this calculation, see Appendix D +of the following reference: +Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015). +Computer Physics Communications, 196, 335-347. diff --git a/examples/SPIN/gneb/interpolate/interpolate.c b/examples/SPIN/gneb/interpolate/interpolate.c index 48804d53a2..39b1b2e192 100644 --- a/examples/SPIN/gneb/interpolate/interpolate.c +++ b/examples/SPIN/gneb/interpolate/interpolate.c @@ -67,8 +67,7 @@ int main() { // reading input file - if((data=fopen("reac_coords_iron_verbose.dat","r")) == NULL) { - //if((data=fopen("neb_init.dat","r")) == NULL) { + if((data=fopen("neb_init.dat","r")) == NULL) { printf("Incorrect input file name."); return 0; } diff --git a/examples/SPIN/gneb/interpolate/reac_coords_iron_verbose.dat b/examples/SPIN/gneb/interpolate/neb_init.dat similarity index 100% rename from examples/SPIN/gneb/interpolate/reac_coords_iron_verbose.dat rename to examples/SPIN/gneb/interpolate/neb_init.dat