Gromacs源码收获（四）
mdrunner函数在runner.c和runner_openmm.c中均有，是MD模拟的主要程序之一。但是对另一个do_md函数的调用一直是个谜，今天终于看出了点头绪。
这里以runner.c中的mdrunner作为例子：
先看一个Interator的定义，在这里我们发现了do_md的影子。
Interator有积分器，综合者的意思
/* The array should match theeI array in include/types/enums.h */
const gmx_intp_t Interator[eiNR] = { {do_md},{do_steep}, {do_cg}, {do_md}, {do_md}, {do_nm}, {do_lbfgs}, {do_tpi}, {do_tpi},{do_md}, {do_md}, {do_md}};
就好奇gmx_intp_t是什么类型的结构，看一下：
typedef struct {
gmx_integrator_t *func;
} gmx_intp_t;
位置就在其定义上面，然后看下gmx_integrator_t的定义：
typedef doublegmx_integrator_t (FILE *log, t_commrec *cr,
int nfile,const t_filenm fnm[],
const output_env_toenv, gmx_bool bVerbose,
gmx_boolbCompact, int nstglobalcomm,
gmx_vsite_t*vsite, gmx_constr_t constr,
int stepout,
t_inputrec*inputrec,
gmx_mtop_t*mtop, t_fcdata *fcd,
t_state*state,
t_mdatoms*mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_ted,
t_forcerec*fr,
intrepl_ex_nst, int repl_ex_nex, int repl_ex_seed,
gmx_membed_t membed,
realcpt_period, real max_hours,
const char*deviceOptions,
unsigned longFlags,
gmx_runtime_t*runtime);
原来是一个方法的typedef声明，那integrator就是eiNR个包含gmx_integrator_t函数的gmx_intp_t结构体数组。有点绕。
通过integrator定义前面的注释，我们找到了eiNR在enums.h中的定义
enum {
eiMD, eiSteep, eiCG, eiBD,eiSD2, eiNM, eiLBFGS, eiTPI, eiTPIC, eiSD1, eiVV, eiVVAK, eiNR
};
但是不理解里面说的match是怎么match的。
下一次对主要嫌疑人的integrator见面在这：
if (integrator[inputrec->eI].func ==do_md)
{
/* Turn on signal handling on all nodes*/
/*
* (A user signal from the PME nodes(if any)
* is communicated to the PP nodes.
*/
signal_handler_install();
}
这里好像注册了一个信号，具体是干什么的，还未知。
然后就是：
/* Now do whatever the userwants us to do (how flexible...) */
integrator[inputrec->eI].func(fplog,cr, nfile, fnm,
oenv,bVerbose, bCompact,
nstglobalcomm,
vsite,constr,
nstepout,inputrec, mtop,
fcd,state,
mdatoms,nrnb, wcycle, ed, fr,
repl_ex_nst, repl_ex_nex, repl_ex_seed,
membed,
cpt_period, max_hours,
deviceOptions,
Flags,
&runtime);
呵呵，找到函数调用了，看一下。首先看看inputrec->eI：
t_inputrec *inputrec; //mdrunner函数中的变量
//结构定义
typedef struct {
int eI; /* Integration method */
gmx_large_int_t nsteps; /* number of steps to be taken */
int simulation_part; /* Used in checkpointing to separatechunks */
gmx_large_int_t init_step; /* start at a stepcount >0 (usedw. tpbconv) */
int nstcalcenergy; /* frequency of energy calc. and T/Pcoupl. upd. */
int cutoff_scheme; /* group or verlet cutoffs */
int ns_type; /* which ns method should weuse? */
int nstlist; /* number of steps beforepairlist is generated */
int ndelta; /* number of cells per rlong */
int nstcomm; /* number of steps after which center of mass */
/* motion is removed */
int comm_mode; /* Center of mass motion removalalgorithm */
int nstcheckpoint; /* checkpointing frequency */
int nstlog; /* number of steps after whichprint to logfile */
int nstxout; /* number of steps after which Xis output */
int nstvout; /* id. for V */
int nstfout; /* id. for F */
int nstenergy; /* number of steps after whichenergies printed */
int nstxtcout; /* id. for compressed trj (.xtc) */
double init_t; /* initial time (ps) */
double delta_t; /* time step (ps) */
real xtcprec; /* precision of xtc file */
real fourier_spacing; /*requested fourier_spacing, when nk? not set */
int nkx, nky, nkz; /* number of k vectors in each spatialdimension*/
/*for fourier methods for long range electrost.*/
int pme_order; /* interpolation order for PME */
real ewald_rtol; /* Real space tolerance for Ewald,determines */
/*the real/reciprocal space relative weight */
int ewald_geometry; /* normal/3d ewald, or pseudo-2d LRcorrections */
real epsilon_surface; /* Epsilon for PME dipole correction */
gmx_bool bOptFFT; /* optimize the fft plan atstart */
int ePBC; /* Type of periodic boundaryconditions */
int bPeriodicMols; /* Periodic molecules */
gmx_bool bContinuation; /* Continuation run: starting state iscorrect */
int etc; /* temperature coupling */
int nsttcouple; /* interval in steps for temperaturecoupling */
gmx_bool bPrintNHChains; /*whether to print nose-hoover chains */
int epc; /* pressure coupling */
int epct; /* pressure coupling type */
int nstpcouple; /* interval in steps for pressurecoupling */
real tau_p; /* pressure coupling time (ps) */
tensor ref_p; /* reference pressure (kJ/(molnm^3)) */
tensor compress; /* compressability ((mol nm^3)/kJ) */
int refcoord_scaling; /* How to scale absolute referencecoordinates */
rvec posres_com; /* The COM of the posres atoms */
rvec posres_comB; /* The B-state COM of the posresatoms */
int andersen_seed; /* Random seed for Andersen thermostat(obsolete) */
real verletbuf_drift; /* Max. drift (kJ/mol/ps/atom) for listbuffer */
real rlist; /* short range pairlist cut-off(nm) */
real rlistlong; /* long range pairlist cut-off (nm) */
int nstcalclr; /* Frequency of evaluating directspace long-range interactions */
real rtpi; /* Radius for test particleinsertion */
int coulombtype; /* Type of electrostaticstreatment */
int coulomb_modifier; /* Modify the Coulomb interaction */
real rcoulomb_switch; /* Coulomb switch range start (nm) */
real rcoulomb; /* Coulomb cutoff (nm) */
real epsilon_r; /* relative dielectricconstant */
real epsilon_rf; /* relative dielectric constant ofthe RF */
int implicit_solvent; /* No (=explicit water), or GBSA solventmodels */
int gb_algorithm; /* Algorithm to use for calculationBorn radii */
int nstgbradii; /* Frequency of updating GeneralizedBorn radii */
real rgbradii; /* Cutoff for GB radiicalculation */
real gb_saltconc; /* Salt concentration (M) for GBSAmodels */
real gb_epsilon_solvent; /* dielectric coeff. of implicitsolvent */
real gb_obc_alpha; /* 1st scaling factor for Bashford-CaseGB */
real gb_obc_beta; /* 2nd scaling factor forBashford-Case GB */
real gb_obc_gamma; /* 3rd scaling factor forBashford-Case GB */
real gb_dielectric_offset; /* Dielectricoffset for Still/HCT/OBC */
int sa_algorithm; /* Algorithm for SA part of GBSA */
real sa_surface_tension; /* Energy factor for SA part of GBSA */
int vdwtype; /* Type of Van der Waalstreatment */
int vdw_modifier; /* Modify the VdW interaction */
real rvdw_switch; /* Van der Waals switch range start(nm) */
real rvdw; /* Van der Waals cutoff (nm) */
int eDispCorr; /* Perform Long range dispersioncorrections */
real tabext; /* Extension of the table beyondthe cut-off, *
* as well asthe table length for 1-4 interac. */
real shake_tol; /* tolerance for shake */
int efep; /* free energycalculations */
t_lambda *fepvals; /* Data for the FEP state */
gmx_bool bSimTemp; /* Whether to do simulatedtempering */
t_simtemp *simtempvals; /* Variables for simulated tempering */
gmx_bool bExpanded; /* Whether expanded ensembles areused */
t_expanded *expandedvals; /* Expanded ensemble parameters */
int eDisre; /* Type of distancerestraining */
real dr_fc; /* force constant for ta_disre */
int eDisreWeighting; /* type of weighting of pairs in onerestraints */
gmx_bool bDisreMixed; /* Use comb of time averaged andinstan. viol's */
int nstdisreout; /* frequency of writing pairdistances to enx */
real dr_tau; /* time constant for memoryfunction in disres */
real orires_fc; /* force constant for orientationalrestraints */
real orires_tau; /* time constant for memory functionin orires */
int nstorireout; /* frequency of writing tr(SD) toenx */
real dihre_fc; /* force constant for dihedralrestraints (obsolete) */
real em_stepsize; /* The stepsize for updating */
real em_tol; /* The tolerance */
int niter; /* Number of iterations forconvergence of */
/*steepest descent in relax_shells */
real fc_stepsize; /* Stepsize for directionalminimization */
/* inrelax_shells */
int nstcgsteep; /* number of steps after which asteepest */
/*descents step is done while doing cg */
int nbfgscorr; /* Number of corrections to thehessian to keep */
int eConstrAlg; /* Type of constraint algorithm */
int nProjOrder; /* Order of the LINCS ProjectionAlgorithm */
real LincsWarnAngle; /* If bond rotates more than %g degrees,warn */
int nLincsIter; /* Number of iterations in the finalLincs step */
gmx_bool bShakeSOR; /* Use successive overrelaxationfor shake */
real bd_fric; /* Friction coefficient for BD(amu/ps) */
int ld_seed; /* Random seed for SD and BD */
int nwall; /* The number of walls */
int wall_type; /* The type of walls */
real wall_r_linpot; /* The potentail is linear forr<=wall_r_linpot */
int wall_atomtype[2]; /* The atom type for walls */
real wall_density[2]; /* Number density for walls */
real wall_ewald_zfac; /*Scaling factor for the box for Ewald */
int ePull; /* Type of pulling: no,umbrella or constraint */
t_pull *pull; /* The data for center of masspulling */
gmx_bool bRot; /* Calculate enforced rotationpotential(s)? */
t_rot *rot; /* The data for enforcedrotation potentials */
real cos_accel; /* Acceleration for viscositycalculation */
tensor deform; /* Triclinic deformationvelocities (nm/ps) */
int userint1; /* User determined parameters */
int userint2;
int userint3;
int userint4;
real userreal1;
real userreal2;
real userreal3;
real userreal4;
t_grpopts opts; /* Group options */
t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
t_cosines et[DIM]; /* Electric field stuff (time part) */
gmx_bool bQMMM; /* QM/MM calculation */
int QMconstraints; /* constraints onQM bonds */
int QMMMscheme; /* Scheme: ONIOM or normal */
real scalefactor; /* factor for scaling the MM charges in QMcalc.*/
/* parameterneeded for AdResS simulation */
gmx_bool bAdress; /* Is AdResS enabled ? */
t_adress *adress; /* The data for adress simulations */
} t_inputrec;
然后调用对应的func函数完成函数调用，但是还有一个疑问inputrec的初始化和值的标定在哪里？继续找
snew(inputrec, 1);这里是申请空间。
这里
* Read (nearly) all datarequired for the simulation */
read_tpx_state(ftp2fn(efTPX, nfile,fnm), inputrec, state, NULL, mtop);
看下t_filenm的定义：
typedef struct {
int ftp; /* File type (see enum above) */
const char *opt; /* Command line option */
const char *fn; /* File name (as set insource code) */
unsigned long flag; /* Flag for all kinds of info (see defs)*/
int nfiles; /* number of files */
char **fns; /* File names */
} t_filenm;
总之是读取一个类型的文件，然后通过文件初始化。
通过Gromacs网站了解到调用的方法取决于mdp文件中的整型量。但是一般情况是调用的do_md方法。