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The question about the output file of System.Name.md Date: 2016/06/03 02:53 Name: Xiangyang Peng   <xiangyang_peng@xtu.edu.cn> Dear openmx authors and users, I am using openmx3.8 to do the molecular dynamics calculations. There is an output file xxx.md containing the position and velocity of all atoms at each time step. I would like to know more details of this file. The fowllowing is a part of a xxx.md file. Si 21.35550 22.05600 32.07300 0.00545 0.06732 0.00025 1476.24715 -458.32608 1228.51120 -0.62712 0.00000 0.00000 0.00000 According to my understanding, Si is the symbol of the atom. The 1st, 2nd and 3rd numbers "21.35550 22.05600 32.07300" are the cartesian coordinates of this atom. The 7th, 8th and 9th numbers "1476.24715 -458.32608 1228.51120" are the velocity of this atom. I would like to know very much the meaning of the remaining numbers, namely, the 4th, 5th and 6th numbers " 0.00545 0.06732 0.00025" and the numbers from 10th to 13th " -0.62712 0.00000 0.00000 0.00000 ". Thank you very much for your help! Best regards

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Re: The question about the output file of System.Name.md ( No.1 ) Date: 2016/06/05 11:37 Name: T. Ozaki Hi, The lines 131th-141th in 'iterout.c' correspond to outputting of the information as fprintf(fp,"%4s %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f\n", Atom_Symbol[j], Gxyz[k][1]*BohrR,Gxyz[k][2]*BohrR,Gxyz[k][3]*BohrR, -Gxyz[k][17],-Gxyz[k][18],-Gxyz[k][19], /* force */ Gxyz[k][24]/(0.4571028*0.000001), /* x-component of velocity */ Gxyz[k][25]/(0.4571028*0.000001), /* y-component of velocity */ Gxyz[k][26]/(0.4571028*0.000001), /* z-component of velocity */ Spe_Core_Charge[i]-(InitN_USpin[k]+InitN_DSpin[k]), /* Net charge, electron charge is defined to be negative. */ InitN_USpin[k]-InitN_DSpin[k], /* magnetic moment (muB) */ angle0,angle1); /* angles of spin */ You may find the following information: 0th symbol: atomic species 1st,2nd, and 3rd numbers: x,y,z-components of atomic coordinates 4th, 5th, and 6th numbers: x,y,z-components of force 7th, 8th, and 9th numbers: x,y,z-components of velocity 10th number: net charge 11th number: magnetic moment (muB) 12th,13th numbers: Euler angles of spin Regards, TO Re: The question about the output file of System.Name.md ( No.2 ) Date: 2016/06/06 19:15 Name: Xiangyang Peng  <xiangyang_peng@xtu.edu.cn> Dear Prof. Ozaki, Thank you very much for your help. I have a further question based on your reply. "10th number: net charge" I do not know how net charge is defined in openmx. I looked into the user's manual of openmx3.8, and found that 'net charge' is only mentioned in the section of '31.3 Electro-static potential fitting'. : In the ESP fitting method an effective point NET CHARGE on each atom is determined by a least square method with constraints so that the sum of the electro-static potential by effective point charges can reproduce electro-static potential calculated by the DFT calculation as much as possible. I would like to ask if the net charge shown in the xxx.md file is obtained by ESP fitting. If it is not, I woulk like to ask how the net charge shown in xxx.md file is defined. Thank you very much for your help. Best regards Re: The question about the output file of System.Name.md ( No.3 ) Date: 2016/06/07 20:49 Name: T. Ozaki Hi, The net charge stored in the md file is defined by Z-N, where Z is the number of valence electrons taken into account in the pseudopotetial, and N is Mulliken population. Regards, TO Re: The question about the output file of System.Name.md ( No.4 ) Date: 2016/06/08 01:10 Name: Xiangyang Peng  <xiangyang_peng@xtu.edu.cn> Dear Prof. Ozaki, Thank you very much for your help. Kind regards

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