nezix / quickses Goto Github PK

I wasn't sure if this is a typo here:

https://github.com/nezix/QuickSES/blob/master/CudaSurf.h#L70

radiusDic['S'] = 2.27f * factor;

For Sulfur, VDW radius is a bit less around 1.8A, whereas sodium is 2.27A.

I recently wrote a Python binding for surface generation. During the test, I found that there are usually some unexpected spikes on the surface as demonstrated in Fig1. Another problem is that the surface is not watertight as demonstrated in Fig2. Did you ever experienced such a situation? Is it like a bug in the program or setting?

Fig1

Fig2

When trying to compile this interesting package with the supplied make file, i run into the following error:

nvcc -c -o CudaSurf.o CudaSurf.cu -Icpdb/ -use_fast_math -O3
nvcc -c -o SmoothMesh.o SmoothMesh.cpp -O3
nvcc -o QuickSES -O3 cpdb/cpdb.o cpdb/utils.o SmoothMesh.o CudaSurf.o
nvlink fatal   : Could not find fatbin in 'cpdb/cpdb.o'
nvlink fatal   : elfLink internal error

Could you please solve this, so that I can try out your package?