Lemina
A molecular dynamics package for network, granular material and point particles with a range of interaction potential.
 
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WriteRestartBinary.c
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1/*
2 * This file is part of Lamina.
3 *
4 * Lamina is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * Lamina is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with Lamina. If not, see <https://www.gnu.org/licenses/>.
16
17 Copyright (C) 2025 Harish Charan, University of Durham, UK
18
19 */
20
21
22#include <stdio.h>
23#include <stdlib.h>
24#include <string.h>
25#include "global.h"
26
27// Header struct must match that of WriteRestartBinary
28typedef struct {
29 char magic[8]; // "LAMINA\0"
30 double version;
31 double timeNow;
32 int nAtom;
33 int nBond;
34 int nAtomType;
35 int nBondType;
36 double regionX; // = region[1]
37 double regionY; // = region[2]
39 int nAtomBlock;
41 double bigDiameter;
42 double InterfaceWidth;
43 int nPairActive;
44 int nPairTotal;
45 double uSumPair;
46 double virSumPair;
47 double virSumPairxx;
48 double virSumPairyy;
49 double virSumPairxy;
50 double TotalBondEnergy;
51 double virSumBond;
52 double virSumBondxx;
53 double virSumBondyy;
54 double virSumBondxy;
55 int stepCount;
56 double forceSumxExtern;
57 double forceSumyExtern;
59
61 RestartHeader hdr = {
62 .magic = "LAMINA",
63 .version = 1.0,
64 .timeNow = timeNow,
65 .nAtom = nAtom,
66 .nBond = nBond,
67 .nAtomType = nAtomType,
68 .nBondType = nBondType,
69 .regionX = region[1],
70 .regionY = region[2],
71 .nAtomInterface = nAtomInterface,
72 .nAtomBlock = nAtomBlock,
73 .nDiscInterface = nDiscInterface,
74 .bigDiameter = bigDiameter,
75 .InterfaceWidth = InterfaceWidth,
76 .nPairActive = nPairActive,
77 .nPairTotal = nPairTotal,
78 .uSumPair = uSumPair,
79 .virSumPair = virSumPair,
80 .virSumPairxx = virSumPairxx,
81 .virSumPairyy = virSumPairyy,
82 .virSumPairxy = virSumPairxy,
83 .TotalBondEnergy = TotalBondEnergy,
84 .virSumBond = virSumBond,
85 .virSumBondxx = virSumBondxx,
86 .virSumBondyy = virSumBondyy,
87 .virSumBondxy = virSumBondxy,
88 .stepCount = stepCount,
89 .forceSumxExtern = forceSumxExtern,
90 .forceSumyExtern = forceSumyExtern
91 };
92
93 char DUMP[256];
94 FILE *fp;
95 sprintf(DUMP, "%s.bin", prefix); // Produces e.g. "../output/test.bin"
96 fp = fopen(DUMP, "wb");
97 if (!fp) {
98 fprintf(stderr, "Error opening binary restart file %s for writing\n", DUMP);
99 exit(EXIT_FAILURE);
100 }
101
102 //Here we are writing the data to binary file
103 fwrite(&hdr, sizeof(RestartHeader), 1, fp);
104 fwrite(&atomID[1], sizeof(int), nAtom, fp);
105 fwrite(&molID[1], sizeof(int), nAtom, fp);
106 fwrite(&atomType[1], sizeof(int), nAtom, fp);
107 fwrite(&atomRadius[1], sizeof(double), nAtom, fp);
108 fwrite(&rx[1], sizeof(double), nAtom, fp);
109 fwrite(&ry[1], sizeof(double), nAtom, fp);
110 fwrite(&vx[1], sizeof(double), nAtom, fp);
111 fwrite(&vy[1], sizeof(double), nAtom, fp);
112 fwrite(&ax[1], sizeof(double), nAtom, fp);
113 fwrite(&ay[1], sizeof(double), nAtom, fp);
114 fwrite(&fx[1], sizeof(double), nAtom, fp);
115 fwrite(&fy[1], sizeof(double), nAtom, fp);
116 fwrite(&atomMass[1], sizeof(double), nAtom, fp);
117 fwrite(&discDragx[1], sizeof(double), nAtom, fp);
118 fwrite(&discDragy[1], sizeof(double), nAtom, fp);
119 fwrite(&atomIDInterface[1], sizeof(int), nAtomInterface, fp);
120
121 fwrite(&BondID[1], sizeof(int), nBond, fp);
122 fwrite(&BondType[1], sizeof(int), nBond, fp);
123 fwrite(&atom1[1], sizeof(int), nBond, fp);
124 fwrite(&atom2[1], sizeof(int), nBond, fp);
125 fwrite(&kb[1], sizeof(double), nBond, fp);
126 fwrite(&ro[1], sizeof(double), nBond, fp);
127 fwrite(&BondEnergy[1], sizeof(double), nBond, fp);
128 fwrite(&BondLength[1], sizeof(double), nBond, fp);
129 fwrite(&nodeDragx[1], sizeof(double), nAtom, fp);
130 fwrite(&nodeDragy[1], sizeof(double), nAtom, fp);
131 fwrite(&rxUnwrap[1], sizeof(double), nAtom, fp);
132 fwrite(&ryUnwrap[1], sizeof(double), nAtom, fp);
133 fwrite(&ImageX[1], sizeof(int), nAtom, fp);
134 fwrite(&ImageY[1], sizeof(int), nAtom, fp);
135
136 fwrite(&PairID[1], sizeof(int), nPairActive, fp);
137 fwrite(&Pairatom1[1], sizeof(int), nPairActive, fp);
138 fwrite(&Pairatom2[1], sizeof(int), nPairActive, fp);
139 fwrite(&PairXij[1], sizeof(double), nPairActive, fp);
140 fwrite(&PairYij[1], sizeof(double), nPairActive, fp);
141
142 fclose(fp);
143}
144
void WriteBinaryRestart()
double virSumBond
int nAtom
Definition global.h:24
int * BondID
double * discDragy
Definition global.h:42
int nDiscInterface
Definition global.h:76
double * atomMass
double virSumPairyy
Definition global.h:88
int nAtomBlock
Definition global.h:76
double virSumPair
Definition global.h:88
int nPairTotal
int * atom2
Definition global.h:36
int * BondType
Definition global.h:37
int nBondType
Definition global.h:35
int nAtomType
double InterfaceWidth
double region[2+1]
double virSumPairxx
Definition global.h:88
int nPairActive
Definition global.h:62
int * molID
double virSumBondxy
Definition global.h:89
double * ay
Definition global.h:17
double * vx
Definition global.h:17
int * ImageX
int * ImageY
Definition global.h:50
int nAtomInterface
double * ro
Definition global.h:38
double * BondLength
Definition global.h:39
int * atomIDInterface
int * atom1
double * rx
double * ax
Definition global.h:17
double * fy
Definition global.h:17
int nBond
double * BondEnergy
double bigDiameter
Definition global.h:75
double * kb
double uSumPair
int * PairID
double * PairXij
double * ryUnwrap
Definition global.h:51
double * nodeDragy
Definition global.h:42
double * atomRadius
double virSumBondxx
Definition global.h:89
double timeNow
Definition global.h:20
int * Pairatom2
Definition global.h:63
int stepCount
Definition global.h:24
double forceSumyExtern
Definition global.h:53
double TotalBondEnergy
double * PairYij
Definition global.h:64
double * discDragx
char * prefix
Definition main.c:13
int * atomType
double * vy
Definition global.h:17
double * rxUnwrap
double * nodeDragx
Definition global.h:42
double virSumBondyy
Definition global.h:89
int * atomID
double forceSumxExtern
Definition global.h:53
double virSumPairxy
Definition global.h:88
double * fx
Definition global.h:17
int * Pairatom1
Definition global.h:63
double * ry
Definition global.h:17